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- {"config":{"lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"OLC Bioinformatics AzureStorage tools This suite of tools (written in Python) allows you to manipulate containers/files/folders in your Azure storage account. There are nine scripts in this package: AzureCredentials : enter, modify, or delete your Azure connection string and account name into your system keyring, avoiding storing plain text passwords, environmental variables, and entering the connection string every time you run one of the scripts in the package AzureUpload : upload a file or folder to a container in your Azure storage account AzureSAS : create SAS (shared access signature) URLs for a file, a folder, or an entire container in your Azure storage account. AzureMove : move a file, folder, or an entire container within your Azure storage account AzureDownload : download a file, folder, or an entire container from your Azure storage account AzureTier : set the storage tier of a file, folder, or an entire container from your Azure storage account AzureDelete : delete a file, folder, or an entire container from your Azure storage account AzureAutomate : run upload, sas, move, download, set_tier, and/or delete in batch AzureList : List and optionally filter containers and/or files in your Azure storage account Feedback If you encounter any issues installing or running AzureStorage, have feature requests, or need assistance, please open an issue on GitHub , or email me at adam.koziol@inspection.gc.ca","title":"Home"},{"location":"#olc-bioinformatics-azurestorage-tools","text":"This suite of tools (written in Python) allows you to manipulate containers/files/folders in your Azure storage account. There are nine scripts in this package: AzureCredentials : enter, modify, or delete your Azure connection string and account name into your system keyring, avoiding storing plain text passwords, environmental variables, and entering the connection string every time you run one of the scripts in the package AzureUpload : upload a file or folder to a container in your Azure storage account AzureSAS : create SAS (shared access signature) URLs for a file, a folder, or an entire container in your Azure storage account. AzureMove : move a file, folder, or an entire container within your Azure storage account AzureDownload : download a file, folder, or an entire container from your Azure storage account AzureTier : set the storage tier of a file, folder, or an entire container from your Azure storage account AzureDelete : delete a file, folder, or an entire container from your Azure storage account AzureAutomate : run upload, sas, move, download, set_tier, and/or delete in batch AzureList : List and optionally filter containers and/or files in your Azure storage account","title":"OLC Bioinformatics AzureStorage tools"},{"location":"#feedback","text":"If you encounter any issues installing or running AzureStorage, have feature requests, or need assistance, please open an issue on GitHub , or email me at adam.koziol@inspection.gc.ca","title":"Feedback"},{"location":"automate/","text":"AzureAutomate Perform multiple upload, SAS URL creation, move, download, storage tier setting, or delete actions. Alternatively, perform multiple actions in a single call Choose either the upload , sas , move , download , tier , delete , or batch functionality General usage usage: AzureAutomate [-h] {upload,sas,move,download,tier,delete,batch} ... Automate the submission of multiple AzureStorage commands optional arguments: -h, --help show this help message and exit Available functionality: {upload,sas,move,download,tier,delete,batch} upload Upload files/folders to Azure storage sas Create SAS URLs for containers/files/folders in Azure storage move Move containers/files/folders in Azure storage download Download containers/files/folders in Azure storage tier Set the storage tier of containers/files/folders in Azure storage delete Delete containers/files/folders in Azure storage batch Perform multiple different operations in batch AzureAutomate upload Choose either the file or folder functionality General usage usage: AzureAutomate upload [-h] {file,folder} ... Upload files/folders to Azure storage optional arguments: -h, --help show this help message and exit Upload functionality: {file,folder} file Upload files to Azure storage folder Upload folders to Azure storage AzureAutomate upload file Automate the upload of multiple files to your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, file name, destination path (optional), storage tier (optional) For additional details on running file uploads, please see the AzureUpload file section Usage usage: AzureAutomate upload file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Upload files to Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, destination path (optional), storage tier (optional) AzureAutomate upload folder Automate the upload of multiple folders to your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, folder name, destination path (optional), storage tier (optional) For additional details on running folder uploads, please see the AzureUpload folder section Usage usage: AzureAutomate upload folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Upload folders to Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields (one entry per line): container name, folder name, destination path (optional), storage tier (optional) AzureAutomate sas Choose either the container , file , or folder functionality General usage usage: AzureAutomate sas [-h] {container,file,folder} ... Create SAS URLs for containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit SAS URL creation functionality: {container,file,folder} container Create SAS URLs for containers in Azure storage file Create SAS URLs for files in Azure storage folder Create SAS URLs for folders in Azure storage AzureAutomate sas container Automate the creation of SAS URLs for multiple containers in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, expiry (optional), output file (optional) For additional details on creating SAS URLs for containers, please see the AzureSAS container section Usage usage: AzureAutomate sas container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, expiry (optional), output file (optional) AzureAutomate sas file Automate the creation of SAS URLs for multiple files in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, file name and path, expiry (optional), output file (optional) For additional details on creating SAS URLs for files, please see the AzureSAS file section Usage usage: AzureAutomate sas file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name and path, expiry (optional), output file (optional) AzureAutomate sas folder Automate the creation of SAS URLs for multiple folders in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, folder name and path, expiry (optional), output file (optional) For additional details on creating SAS URLs for folders, please see the AzureSAS folder section Usage usage: AzureAutomate sas folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name and path, expiry (optional), output file (optional) AzureAutomate move Choose either the container , file , or folder functionality General usage usage: AzureAutomate move [-h] {container,file,folder} ... Move containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Move functionality: {container,file,folder} container Move containers in Azure storage file Move files in Azure storage folder Move folders in Azure storage AzureAutomate move container Automate the moving of multiple containers in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, target container, destination path (optional), storage tier (optional) For additional details on moving containers, please see the AzureMove container section Usage usage: AzureAutomate move container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, destination path (optional), storage tier (optional) AzureAutomate move file Automate the moving of multiple files in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, target container, file name, destination path (optional), storage tier (optional) For additional details on moving files, please see the AzureMove file section Usage usage: AzureAutomate move file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, file name, destination path (optional), storage tier (optional) AzureAutomate move folder Automate the moving of multiple folders in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, target container, folder name, destination path (optional), storage tier (optional) For additional details on moving folders, please see the AzureMove folder section Usage usage: AzureAutomate move folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, folder name, destination path (optional), storage tier (optional) AzureAutomate download Choose either the container , file , or folder functionality General usage usage: AzureAutomate download [-h] {container,file,folder} ... Download containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Download functionality: {container,file,folder} container Download containers from Azure storage file Download files from Azure storage folder Download folders from Azure storage AzureAutomate download container Automate the downloading of multiple containers from your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, output path (optional) For additional details on downloading containers, please see the AzureDownload container section Usage usage: AzureAutomate download container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download containers from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, output path (optional) AzureAutomate download file Automate the downloading of multiple files from your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, file name, output path (optional) For additional details on downloading files, please see the AzureDownload file section Usage usage: AzureAutomate download file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download files from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, output path (optional) AzureAutomate download folder Automate the downloading of multiple folders from your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, folder name, output path (optional) For additional details on downloading folders, please see the AzureDownload folder section Usage usage: AzureAutomate download folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download folders from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, output path (optional) AzureAutomate tier Choose either the container , file , or folder functionality General usage usage: AzureAutomate tier [-h] {container,file,folder} ... Set the storage tier of containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Storage tier setting functionality: {container,file,folder} container Set the storage tier of containers in Azure storage file Set the storage tier of files in Azure storage folder Set the storage tier of folders in Azure storage AzureAutomate tier container Automate setting the storage tier for multiple containers in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, storage tier For additional details on setting the storage tier of containers, please see the AzureTier container section Usage usage: AzureAutomate tier container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, storage tier AzureAutomate tier file Automate setting the storage tier for multiple files in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, file name, storage tier For additional details on setting the storage tier of files, please see the AzureTier file section Usage usage: AzureAutomate tier file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, storage tier AzureAutomate tier folder Automate setting the storage tier for multiple folders in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, folder name, storage tier For additional details on setting the storage tier of folders, please see the AzureTier folder section Usage usage: AzureAutomate tier folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, storage tier AzureAutomate delete Choose either the container , file , or folder functionality General usage usage: AzureAutomate delete [-h] {container,file,folder} ... Delete containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Delete functionality: {container,file,folder} container Delete containers in Azure storage file Delete files in Azure storage folder Delete folders in Azure storage AzureAutomate delete container Automate deleting multiple containers in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format File with the following field: container name For additional details on deleting containers, please see the AzureDelete container section Usage usage: AzureAutomate delete container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE File with the following field: container name AzureAutomate delete file Automate deleting multiple files in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, file name, retention time (optional) For additional details on deleting files, please see the AzureDelete file section Usage usage: AzureAutomate delete file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, retention time (optional) AzureAutomate delete folder Automate deleting multiple folders in your Azure storage account Required arguments: container name account name name and path of batch file Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Batch file format Tab-separated file with the following fields: container name, folder name, retention time (optional) For additional details on deleting folders, please see the AzureDelete folder section Usage usage: AzureAutomate delete folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, retention time (optional) AzureAutomate batch Automate multiple operations Batch file format Tab-separated file in the following format: command, sub-command, command:subcommand-specific arguments Please review the AzureAutomate documentation for all the possible operations Usage usage: AzureAutomate batch [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Perform multiple different operations in batch optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file in the following format: command, sub-command, arguments Below is the complete list of functionalities: upload, file, container name, file name, destination path (optional), storage tier (optional) upload, folder, container name, folder name, destination path (optional), storage tier (optional) sas, container, container name, expiry (optional), output file (optional) sas, file, container name, file name and path, expiry (optional), output file (optional) sas, folder, container name, folder name and path, expiry (optional), output file (optional) move, container, container name, target container, destination path (optional), storage tier (optional) move, file, container name, target container, file name, destination path (optional), storage tier (optional) move, folder, container name, target container, folder name, destination path (optional), storage tier (optional) download, container, container name, output path (optional) download, file, container name, file name, output path (optional) download, folder, container name, folder name, output path (optional) tier, container, container name, storage tier tier, file, container name, file name, storage tier tier, folder, container name, folder name, storage tier delete, container, container name delete, file, container name, file name, retention time (optional) delete, folder, container name, folder name, retention time (optional)","title":"Automate"},{"location":"automate/#azureautomate","text":"Perform multiple upload, SAS URL creation, move, download, storage tier setting, or delete actions. Alternatively, perform multiple actions in a single call Choose either the upload , sas , move , download , tier , delete , or batch functionality","title":"AzureAutomate"},{"location":"automate/#general-usage","text":"usage: AzureAutomate [-h] {upload,sas,move,download,tier,delete,batch} ... Automate the submission of multiple AzureStorage commands optional arguments: -h, --help show this help message and exit Available functionality: {upload,sas,move,download,tier,delete,batch} upload Upload files/folders to Azure storage sas Create SAS URLs for containers/files/folders in Azure storage move Move containers/files/folders in Azure storage download Download containers/files/folders in Azure storage tier Set the storage tier of containers/files/folders in Azure storage delete Delete containers/files/folders in Azure storage batch Perform multiple different operations in batch","title":"General usage"},{"location":"automate/#azureautomate-upload","text":"Choose either the file or folder functionality","title":"AzureAutomate upload"},{"location":"automate/#general-usage_1","text":"usage: AzureAutomate upload [-h] {file,folder} ... Upload files/folders to Azure storage optional arguments: -h, --help show this help message and exit Upload functionality: {file,folder} file Upload files to Azure storage folder Upload folders to Azure storage","title":"General usage"},{"location":"automate/#azureautomate-upload-file","text":"Automate the upload of multiple files to your Azure storage account","title":"AzureAutomate upload file"},{"location":"automate/#required-arguments","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format","text":"Tab-separated file with the following fields: container name, file name, destination path (optional), storage tier (optional) For additional details on running file uploads, please see the AzureUpload file section","title":"Batch file format"},{"location":"automate/#usage","text":"usage: AzureAutomate upload file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Upload files to Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, destination path (optional), storage tier (optional)","title":"Usage"},{"location":"automate/#azureautomate-upload-folder","text":"Automate the upload of multiple folders to your Azure storage account","title":"AzureAutomate upload folder"},{"location":"automate/#required-arguments_1","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_1","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_1","text":"Tab-separated file with the following fields: container name, folder name, destination path (optional), storage tier (optional) For additional details on running folder uploads, please see the AzureUpload folder section","title":"Batch file format"},{"location":"automate/#usage_1","text":"usage: AzureAutomate upload folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Upload folders to Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields (one entry per line): container name, folder name, destination path (optional), storage tier (optional)","title":"Usage"},{"location":"automate/#azureautomate-sas","text":"Choose either the container , file , or folder functionality","title":"AzureAutomate sas"},{"location":"automate/#general-usage_2","text":"usage: AzureAutomate sas [-h] {container,file,folder} ... Create SAS URLs for containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit SAS URL creation functionality: {container,file,folder} container Create SAS URLs for containers in Azure storage file Create SAS URLs for files in Azure storage folder Create SAS URLs for folders in Azure storage","title":"General usage"},{"location":"automate/#azureautomate-sas-container","text":"Automate the creation of SAS URLs for multiple containers in your Azure storage account","title":"AzureAutomate sas container"},{"location":"automate/#required-arguments_2","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_2","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_2","text":"Tab-separated file with the following fields: container name, expiry (optional), output file (optional) For additional details on creating SAS URLs for containers, please see the AzureSAS container section","title":"Batch file format"},{"location":"automate/#usage_2","text":"usage: AzureAutomate sas container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, expiry (optional), output file (optional)","title":"Usage"},{"location":"automate/#azureautomate-sas-file","text":"Automate the creation of SAS URLs for multiple files in your Azure storage account","title":"AzureAutomate sas file"},{"location":"automate/#required-arguments_3","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_3","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_3","text":"Tab-separated file with the following fields: container name, file name and path, expiry (optional), output file (optional) For additional details on creating SAS URLs for files, please see the AzureSAS file section","title":"Batch file format"},{"location":"automate/#usage_3","text":"usage: AzureAutomate sas file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name and path, expiry (optional), output file (optional)","title":"Usage"},{"location":"automate/#azureautomate-sas-folder","text":"Automate the creation of SAS URLs for multiple folders in your Azure storage account","title":"AzureAutomate sas folder"},{"location":"automate/#required-arguments_4","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_4","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_4","text":"Tab-separated file with the following fields: container name, folder name and path, expiry (optional), output file (optional) For additional details on creating SAS URLs for folders, please see the AzureSAS folder section","title":"Batch file format"},{"location":"automate/#usage_4","text":"usage: AzureAutomate sas folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Create SAS URLs for folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name and path, expiry (optional), output file (optional)","title":"Usage"},{"location":"automate/#azureautomate-move","text":"Choose either the container , file , or folder functionality","title":"AzureAutomate move"},{"location":"automate/#general-usage_3","text":"usage: AzureAutomate move [-h] {container,file,folder} ... Move containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Move functionality: {container,file,folder} container Move containers in Azure storage file Move files in Azure storage folder Move folders in Azure storage","title":"General usage"},{"location":"automate/#azureautomate-move-container","text":"Automate the moving of multiple containers in your Azure storage account","title":"AzureAutomate move container"},{"location":"automate/#required-arguments_5","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_5","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_5","text":"Tab-separated file with the following fields: container name, target container, destination path (optional), storage tier (optional) For additional details on moving containers, please see the AzureMove container section","title":"Batch file format"},{"location":"automate/#usage_5","text":"usage: AzureAutomate move container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, destination path (optional), storage tier (optional)","title":"Usage"},{"location":"automate/#azureautomate-move-file","text":"Automate the moving of multiple files in your Azure storage account","title":"AzureAutomate move file"},{"location":"automate/#required-arguments_6","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_6","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_6","text":"Tab-separated file with the following fields: container name, target container, file name, destination path (optional), storage tier (optional) For additional details on moving files, please see the AzureMove file section","title":"Batch file format"},{"location":"automate/#usage_6","text":"usage: AzureAutomate move file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, file name, destination path (optional), storage tier (optional)","title":"Usage"},{"location":"automate/#azureautomate-move-folder","text":"Automate the moving of multiple folders in your Azure storage account","title":"AzureAutomate move folder"},{"location":"automate/#required-arguments_7","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_7","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_7","text":"Tab-separated file with the following fields: container name, target container, folder name, destination path (optional), storage tier (optional) For additional details on moving folders, please see the AzureMove folder section","title":"Batch file format"},{"location":"automate/#usage_7","text":"usage: AzureAutomate move folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Move folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, target container, folder name, destination path (optional), storage tier (optional)","title":"Usage"},{"location":"automate/#azureautomate-download","text":"Choose either the container , file , or folder functionality","title":"AzureAutomate download"},{"location":"automate/#general-usage_4","text":"usage: AzureAutomate download [-h] {container,file,folder} ... Download containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Download functionality: {container,file,folder} container Download containers from Azure storage file Download files from Azure storage folder Download folders from Azure storage","title":"General usage"},{"location":"automate/#azureautomate-download-container","text":"Automate the downloading of multiple containers from your Azure storage account","title":"AzureAutomate download container"},{"location":"automate/#required-arguments_8","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_8","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_8","text":"Tab-separated file with the following fields: container name, output path (optional) For additional details on downloading containers, please see the AzureDownload container section","title":"Batch file format"},{"location":"automate/#usage_8","text":"usage: AzureAutomate download container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download containers from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, output path (optional)","title":"Usage"},{"location":"automate/#azureautomate-download-file","text":"Automate the downloading of multiple files from your Azure storage account","title":"AzureAutomate download file"},{"location":"automate/#required-arguments_9","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_9","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_9","text":"Tab-separated file with the following fields: container name, file name, output path (optional) For additional details on downloading files, please see the AzureDownload file section","title":"Batch file format"},{"location":"automate/#usage_9","text":"usage: AzureAutomate download file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download files from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, output path (optional)","title":"Usage"},{"location":"automate/#azureautomate-download-folder","text":"Automate the downloading of multiple folders from your Azure storage account","title":"AzureAutomate download folder"},{"location":"automate/#required-arguments_10","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_10","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_10","text":"Tab-separated file with the following fields: container name, folder name, output path (optional) For additional details on downloading folders, please see the AzureDownload folder section","title":"Batch file format"},{"location":"automate/#usage_10","text":"usage: AzureAutomate download folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Download folders from Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, output path (optional)","title":"Usage"},{"location":"automate/#azureautomate-tier","text":"Choose either the container , file , or folder functionality","title":"AzureAutomate tier"},{"location":"automate/#general-usage_5","text":"usage: AzureAutomate tier [-h] {container,file,folder} ... Set the storage tier of containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Storage tier setting functionality: {container,file,folder} container Set the storage tier of containers in Azure storage file Set the storage tier of files in Azure storage folder Set the storage tier of folders in Azure storage","title":"General usage"},{"location":"automate/#azureautomate-tier-container","text":"Automate setting the storage tier for multiple containers in your Azure storage account","title":"AzureAutomate tier container"},{"location":"automate/#required-arguments_11","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_11","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_11","text":"Tab-separated file with the following fields: container name, storage tier For additional details on setting the storage tier of containers, please see the AzureTier container section","title":"Batch file format"},{"location":"automate/#usage_11","text":"usage: AzureAutomate tier container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, storage tier","title":"Usage"},{"location":"automate/#azureautomate-tier-file","text":"Automate setting the storage tier for multiple files in your Azure storage account","title":"AzureAutomate tier file"},{"location":"automate/#required-arguments_12","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_12","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_12","text":"Tab-separated file with the following fields: container name, file name, storage tier For additional details on setting the storage tier of files, please see the AzureTier file section","title":"Batch file format"},{"location":"automate/#usage_12","text":"usage: AzureAutomate tier file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, storage tier","title":"Usage"},{"location":"automate/#azureautomate-tier-folder","text":"Automate setting the storage tier for multiple folders in your Azure storage account","title":"AzureAutomate tier folder"},{"location":"automate/#required-arguments_13","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_13","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_13","text":"Tab-separated file with the following fields: container name, folder name, storage tier For additional details on setting the storage tier of folders, please see the AzureTier folder section","title":"Batch file format"},{"location":"automate/#usage_13","text":"usage: AzureAutomate tier folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Set the storage tier of folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, storage tier","title":"Usage"},{"location":"automate/#azureautomate-delete","text":"Choose either the container , file , or folder functionality","title":"AzureAutomate delete"},{"location":"automate/#general-usage_6","text":"usage: AzureAutomate delete [-h] {container,file,folder} ... Delete containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Delete functionality: {container,file,folder} container Delete containers in Azure storage file Delete files in Azure storage folder Delete folders in Azure storage","title":"General usage"},{"location":"automate/#azureautomate-delete-container","text":"Automate deleting multiple containers in your Azure storage account","title":"AzureAutomate delete container"},{"location":"automate/#required-arguments_14","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_14","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_14","text":"File with the following field: container name For additional details on deleting containers, please see the AzureDelete container section","title":"Batch file format"},{"location":"automate/#usage_14","text":"usage: AzureAutomate delete container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete containers in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE File with the following field: container name","title":"Usage"},{"location":"automate/#azureautomate-delete-file","text":"Automate deleting multiple files in your Azure storage account","title":"AzureAutomate delete file"},{"location":"automate/#required-arguments_15","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_15","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_15","text":"Tab-separated file with the following fields: container name, file name, retention time (optional) For additional details on deleting files, please see the AzureDelete file section","title":"Batch file format"},{"location":"automate/#usage_15","text":"usage: AzureAutomate delete file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete files in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, file name, retention time (optional)","title":"Usage"},{"location":"automate/#azureautomate-delete-folder","text":"Automate deleting multiple folders in your Azure storage account","title":"AzureAutomate delete folder"},{"location":"automate/#required-arguments_16","text":"container name account name name and path of batch file","title":"Required arguments:"},{"location":"automate/#optional-arguments_16","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"automate/#batch-file-format_16","text":"Tab-separated file with the following fields: container name, folder name, retention time (optional) For additional details on deleting folders, please see the AzureDelete folder section","title":"Batch file format"},{"location":"automate/#usage_16","text":"usage: AzureAutomate delete folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Delete folders in Azure storage optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file with the following fields: container name, folder name, retention time (optional)","title":"Usage"},{"location":"automate/#azureautomate-batch","text":"Automate multiple operations","title":"AzureAutomate batch"},{"location":"automate/#batch-file-format_17","text":"Tab-separated file in the following format: command, sub-command, command:subcommand-specific arguments Please review the AzureAutomate documentation for all the possible operations","title":"Batch file format"},{"location":"automate/#usage_17","text":"usage: AzureAutomate batch [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE Perform multiple different operations in batch optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -b BATCH_FILE, --batch_file BATCH_FILE Tab-separated file in the following format: command, sub-command, arguments Below is the complete list of functionalities: upload, file, container name, file name, destination path (optional), storage tier (optional) upload, folder, container name, folder name, destination path (optional), storage tier (optional) sas, container, container name, expiry (optional), output file (optional) sas, file, container name, file name and path, expiry (optional), output file (optional) sas, folder, container name, folder name and path, expiry (optional), output file (optional) move, container, container name, target container, destination path (optional), storage tier (optional) move, file, container name, target container, file name, destination path (optional), storage tier (optional) move, folder, container name, target container, folder name, destination path (optional), storage tier (optional) download, container, container name, output path (optional) download, file, container name, file name, output path (optional) download, folder, container name, folder name, output path (optional) tier, container, container name, storage tier tier, file, container name, file name, storage tier tier, folder, container name, folder name, storage tier delete, container, container name delete, file, container name, file name, retention time (optional) delete, folder, container name, folder name, retention time (optional)","title":"Usage"},{"location":"credentials/","text":"AzureCredentials AzureCredentials allows you to store, modify, or delete your Azure account name and connection string in the system keyring Choose either the store or delete functionality Find your connection string Find your account key General Usage usage: AzureCredentials [-h] {store,delete} ... Set, modify, or delete Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit Available functionality: {store,delete} store Store or update Azure storage credentials in the system keyring delete Delete Azure storage credentials in the system keyring Azure credentials store Store or modify your account name and connection string in the system keyring Required arguments: account name Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: To store the account name account_name and your connection string in the system keyring AzureCredentials store -a account_name NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. To store the account name account_name and your connection string in the system keyring using the passphrase passphrase AzureCredentials store -a account_name -p passphrase NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. Usage usage: AzureCredentials store [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Store or update Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. Azure credentials delete Delete your account name and connection string from the system keyring Required arguments: account name Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example command: To delete the account name account_name and your connection string from the system keyring AzureCredentials delete -a account_name NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. To delete the account name account_name and your connection string from the system keyring stored using the passphrase passphrase AzureCredentials delete -a account_name -p passphrase NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. Usage usage: AzureCredentials delete [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Delete Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info.","title":"Credentials"},{"location":"credentials/#azurecredentials","text":"AzureCredentials allows you to store, modify, or delete your Azure account name and connection string in the system keyring Choose either the store or delete functionality Find your connection string Find your account key","title":"AzureCredentials"},{"location":"credentials/#general-usage","text":"usage: AzureCredentials [-h] {store,delete} ... Set, modify, or delete Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit Available functionality: {store,delete} store Store or update Azure storage credentials in the system keyring delete Delete Azure storage credentials in the system keyring","title":"General Usage"},{"location":"credentials/#azure-credentials-store","text":"Store or modify your account name and connection string in the system keyring","title":"Azure credentials store"},{"location":"credentials/#required-arguments","text":"account name","title":"Required arguments:"},{"location":"credentials/#optional-arguments","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"credentials/#example-commands","text":"To store the account name account_name and your connection string in the system keyring AzureCredentials store -a account_name NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. To store the account name account_name and your connection string in the system keyring using the passphrase passphrase AzureCredentials store -a account_name -p passphrase NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.","title":"Example commands:"},{"location":"credentials/#usage","text":"usage: AzureCredentials store [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Store or update Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info.","title":"Usage"},{"location":"credentials/#azure-credentials-delete","text":"Delete your account name and connection string from the system keyring","title":"Azure credentials delete"},{"location":"credentials/#required-arguments_1","text":"account name","title":"Required arguments:"},{"location":"credentials/#optional-arguments_1","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"credentials/#example-command","text":"To delete the account name account_name and your connection string from the system keyring AzureCredentials delete -a account_name NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. To delete the account name account_name and your connection string from the system keyring stored using the passphrase passphrase AzureCredentials delete -a account_name -p passphrase NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.","title":"Example command:"},{"location":"credentials/#usage_1","text":"usage: AzureCredentials delete [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Delete Azure storage credentials in the system keyring optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info.","title":"Usage"},{"location":"delete/","text":"AzureDelete Delete containers, files, or folders from your Azure storage account Choose either the container , file , or folder functionality General usage usage: AzureDelete [-h] {container,file,folder} ... Move and/or delete containers, files, or folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Delete a container in Azure storage file Delete a file in Azure storage folder Delete a folder in Azure storage AzureDelete container Delete a container from your Azure storage account Required arguments: container name account name Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example command: These commands will use container-name as the name of the container and account_name as the name of the storage account To delete a container from your Azure storage account AzureDelete container -a account_name -c container-name Usage usage: AzureDelete container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Delete a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. AzureDelete file Delete a file from your Azure storage account Required arguments: container name account name file name Optional arguments: retention time: time to retain deleted files. Default is 8 days passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container and account_name as the name of the storage account To delete the file file_name.gz from your Azure storage account AzureDelete file -a account_name -c container-name -f file_name.gz To delete the file file_name.gz nested in folder outputs from your Azure storage account, and retain it for 10 days AzureDelete file -a account_name -c container-name -f outputs/file_name.gz -r 10 Usage usage: AzureDelete file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FILE [-r RETENTION_TIME] Delete a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -f FILE, --file FILE Name of blob file to delete in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz -r RETENTION_TIME, --retention_time RETENTION_TIME Retention time for deleted files. Default is 8 days. Must be between 1 and 365 AzureDelete folder Delete a folder from your Azure storage account Required arguments: container name account name folder name Optional arguments: retention time: time to retain deleted files in the folder. Default is 8 days passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container and account_name as the name of the storage account To delete the folder folder_name from your Azure storage account AzureDelete folder -a account_name -c container-name -f folder_name To delete the folder folder_name nested in folder outputs from your Azure storage account, and retain it for 10 days AzureDelete folder -a account_name -c container-name -f outputs/folder_name -r 10 Usage usage: AzureDelete folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FOLDER [-r RETENTION_TIME] Delete a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -f FOLDER, --folder FOLDER Name of folder to delete in Azure storage. e.g. InterOp -r RETENTION_TIME, --retention_time RETENTION_TIME Retention time for deleted files. Default is 8 days","title":"Delete"},{"location":"delete/#azuredelete","text":"Delete containers, files, or folders from your Azure storage account Choose either the container , file , or folder functionality","title":"AzureDelete"},{"location":"delete/#general-usage","text":"usage: AzureDelete [-h] {container,file,folder} ... Move and/or delete containers, files, or folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Delete a container in Azure storage file Delete a file in Azure storage folder Delete a folder in Azure storage","title":"General usage"},{"location":"delete/#azuredelete-container","text":"Delete a container from your Azure storage account","title":"AzureDelete container"},{"location":"delete/#required-arguments","text":"container name account name","title":"Required arguments:"},{"location":"delete/#optional-arguments","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"delete/#example-command","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To delete a container from your Azure storage account AzureDelete container -a account_name -c container-name","title":"Example command:"},{"location":"delete/#usage","text":"usage: AzureDelete container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] Delete a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info.","title":"Usage"},{"location":"delete/#azuredelete-file","text":"Delete a file from your Azure storage account","title":"AzureDelete file"},{"location":"delete/#required-arguments_1","text":"container name account name file name","title":"Required arguments:"},{"location":"delete/#optional-arguments_1","text":"retention time: time to retain deleted files. Default is 8 days passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"delete/#example-commands","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To delete the file file_name.gz from your Azure storage account AzureDelete file -a account_name -c container-name -f file_name.gz To delete the file file_name.gz nested in folder outputs from your Azure storage account, and retain it for 10 days AzureDelete file -a account_name -c container-name -f outputs/file_name.gz -r 10","title":"Example commands:"},{"location":"delete/#usage_1","text":"usage: AzureDelete file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FILE [-r RETENTION_TIME] Delete a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -f FILE, --file FILE Name of blob file to delete in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz -r RETENTION_TIME, --retention_time RETENTION_TIME Retention time for deleted files. Default is 8 days. Must be between 1 and 365","title":"Usage"},{"location":"delete/#azuredelete-folder","text":"Delete a folder from your Azure storage account","title":"AzureDelete folder"},{"location":"delete/#required-arguments_2","text":"container name account name folder name","title":"Required arguments:"},{"location":"delete/#optional-arguments_2","text":"retention time: time to retain deleted files in the folder. Default is 8 days passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"delete/#example-commands_1","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To delete the folder folder_name from your Azure storage account AzureDelete folder -a account_name -c container-name -f folder_name To delete the folder folder_name nested in folder outputs from your Azure storage account, and retain it for 10 days AzureDelete folder -a account_name -c container-name -f outputs/folder_name -r 10","title":"Example commands:"},{"location":"delete/#usage_2","text":"usage: AzureDelete folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FOLDER [-r RETENTION_TIME] Delete a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -f FOLDER, --folder FOLDER Name of folder to delete in Azure storage. e.g. InterOp -r RETENTION_TIME, --retention_time RETENTION_TIME Retention time for deleted files. Default is 8 days","title":"Usage"},{"location":"download/","text":"AzureDownload Download containers, files, or folders from your Azure storage account Choose either the container , file , or folder functionality General usage usage: AzureDownload [-h] {container,file,folder} ... Download containers/files/folders from Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Download a container from Azure storage file Download a file from Azure storage folder Download a folder from Azure storage AzureDownload container Download a container from your Azure storage account Required arguments: container name account name Optional arguments: output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container and account_name as the name of the storage account To perform a basic container download (download to your current working directory) AzureDownload container -a account name -c container-name To download a container to the folder outputs in your current working directory AzureDownload container -a account name -c container-name -o outputs To download a container to the folder /home/users/outputs AzureDownload container -a account name -c container-name -o /home/users/outputs Usage usage: AzureDownload container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] Download a container from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD AzureDownload file Download a file from your Azure storage account Required arguments: container name account name file name Optional arguments: output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container and account_name as the name of the storage account To download the file file_name.gz to your current working directory AzureDownload file -a account name -c container-name -f file_name.gz To download the file file_name.gz nested in the outputs folder to your current working directory AzureDownload file -a account name -c container-name -f outputs/file_name.gz To download the file file_name.gz nested in the outputs folder to the folder files in your current working directory AzureDownload file -a account name -c container-name -f outputs/file_name.gz -o files To download the file file_name.gz to the folder /home/users/outputs AzureDownload file -a account name -c container-name -f file_name.gz -o /home/users/outputs Usage usage: AzureDownload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FILE Download a file from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD -f FILE, --file FILE Name of file to download from Azure storage.e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz AzureDownload folder Download a folder from your Azure storage account Required arguments: container name account name folder name Optional arguments: output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container and account_name as the name of the storage account To download the folder folder_name to your current working directory AzureDownload folder -a account name -c container-name -f folder_name To download the folder folder_name nested in the outputs folder to your current working directory AzureDownload folder -a account name -c container-name -f outputs/folder_name To download the folder folder_name nested in the outputs folder to the folder folders in your current working directory AzureDownload folder -a account name -c container-name -f outputs/folder_name -o folders To download the folder folder_name to the folder /home/users/outputs AzureDownload folder -a account name -c container-name -f folder_name -o /home/users/outputs Usage usage: AzureDownload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FOLDER Download a folder from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD -f FOLDER, --folder FOLDER Name of the folder to download from Azure storage e.g. InterOp","title":"Download"},{"location":"download/#azuredownload","text":"Download containers, files, or folders from your Azure storage account Choose either the container , file , or folder functionality","title":"AzureDownload"},{"location":"download/#general-usage","text":"usage: AzureDownload [-h] {container,file,folder} ... Download containers/files/folders from Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Download a container from Azure storage file Download a file from Azure storage folder Download a folder from Azure storage","title":"General usage"},{"location":"download/#azuredownload-container","text":"Download a container from your Azure storage account","title":"AzureDownload container"},{"location":"download/#required-arguments","text":"container name account name","title":"Required arguments:"},{"location":"download/#optional-arguments","text":"output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"download/#example-commands","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To perform a basic container download (download to your current working directory) AzureDownload container -a account name -c container-name To download a container to the folder outputs in your current working directory AzureDownload container -a account name -c container-name -o outputs To download a container to the folder /home/users/outputs AzureDownload container -a account name -c container-name -o /home/users/outputs","title":"Example commands:"},{"location":"download/#usage","text":"usage: AzureDownload container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] Download a container from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD","title":"Usage"},{"location":"download/#azuredownload-file","text":"Download a file from your Azure storage account","title":"AzureDownload file"},{"location":"download/#required-arguments_1","text":"container name account name file name","title":"Required arguments:"},{"location":"download/#optional-arguments_1","text":"output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"download/#example-commands_1","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To download the file file_name.gz to your current working directory AzureDownload file -a account name -c container-name -f file_name.gz To download the file file_name.gz nested in the outputs folder to your current working directory AzureDownload file -a account name -c container-name -f outputs/file_name.gz To download the file file_name.gz nested in the outputs folder to the folder files in your current working directory AzureDownload file -a account name -c container-name -f outputs/file_name.gz -o files To download the file file_name.gz to the folder /home/users/outputs AzureDownload file -a account name -c container-name -f file_name.gz -o /home/users/outputs","title":"Example commands:"},{"location":"download/#usage_1","text":"usage: AzureDownload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FILE Download a file from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD -f FILE, --file FILE Name of file to download from Azure storage.e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz","title":"Usage"},{"location":"download/#azuredownload-folder","text":"Download a folder from your Azure storage account","title":"AzureDownload folder"},{"location":"download/#required-arguments_2","text":"container name account name folder name","title":"Required arguments:"},{"location":"download/#optional-arguments_2","text":"output path: local path where container is to be saved. Default is your current working directory passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"download/#example-commands_2","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To download the folder folder_name to your current working directory AzureDownload folder -a account name -c container-name -f folder_name To download the folder folder_name nested in the outputs folder to your current working directory AzureDownload folder -a account name -c container-name -f outputs/folder_name To download the folder folder_name nested in the outputs folder to the folder folders in your current working directory AzureDownload folder -a account name -c container-name -f outputs/folder_name -o folders To download the folder folder_name to the folder /home/users/outputs AzureDownload folder -a account name -c container-name -f folder_name -o /home/users/outputs","title":"Example commands:"},{"location":"download/#usage_2","text":"usage: AzureDownload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FOLDER Download a folder from Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_PATH, --output_path OUTPUT_PATH Name and path of directory in which the outputs are to be saved. Default is your $CWD -f FOLDER, --folder FOLDER Name of the folder to download from Azure storage e.g. InterOp","title":"Usage"},{"location":"install/","text":"Installation AzureStorage is available as a conda package, so conda must be installed on your system. Conda Skip this step if you have already installed conda wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda conda update -q conda AzureStorage Create new conda environment conda create -n azure_storage -c olcbioinformatics azure_storage Install in existing Python 3.8.5 environment Install the AzureStorage package: conda install -c olcbioinformatics azure_storage Credentials You must enter your Azure storage connection string and account name into the system keyring before running any of the other scripts Find your connection string Find your account key Once you know your account key and connection string, run: AzureCredentials store Your credentials will be securely stored in the system keyring Tests If you encounter issues with the AzureStorage package, tests are available to ensure that the installation was successful and your credentials are valid. You will need to clone this repository and run the tests with pytest git clone https://github.com/OLC-LOC-Bioinformatics/AzureStorage.git cd AzureStorage python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec","title":"Installation"},{"location":"install/#installation","text":"AzureStorage is available as a conda package, so conda must be installed on your system.","title":"Installation"},{"location":"install/#conda","text":"Skip this step if you have already installed conda wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda conda update -q conda","title":"Conda"},{"location":"install/#azurestorage","text":"","title":"AzureStorage"},{"location":"install/#create-new-conda-environment","text":"conda create -n azure_storage -c olcbioinformatics azure_storage","title":"Create new conda environment"},{"location":"install/#install-in-existing-python-385-environment","text":"Install the AzureStorage package: conda install -c olcbioinformatics azure_storage","title":"Install in existing Python 3.8.5 environment"},{"location":"install/#credentials","text":"You must enter your Azure storage connection string and account name into the system keyring before running any of the other scripts Find your connection string Find your account key Once you know your account key and connection string, run: AzureCredentials store Your credentials will be securely stored in the system keyring","title":"Credentials"},{"location":"install/#tests","text":"If you encounter issues with the AzureStorage package, tests are available to ensure that the installation was successful and your credentials are valid. You will need to clone this repository and run the tests with pytest git clone https://github.com/OLC-LOC-Bioinformatics/AzureStorage.git cd AzureStorage python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec","title":"Tests"},{"location":"list/","text":"AzureList List and optionally filter containers and/or files in your Azure storage account Choose either the container , or the search functionality This script allows you to filter using regular expressions, so make sure you know what you're doing , check out a tutorial , look at a cheatsheet , and/or test your expressions Important: since the regular expressions are being entered on the command line, you will need to escape certain characters e.g. ! should be ! General Usage usage: AzureList [-h] {container,search} ... Explore your Azure storage account optional arguments: -h, --help show this help message and exit Available functionality: {container,search} container Filter and list containers in your Azure storage account search Search files in a container (or containers) in Azure storage AzureList container List and optionally filter containers in your Azure storage account AzureList container required arguments account name AzureList container optional arguments expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! output_file: name and path of file in which the outputs are to be saved. passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info AzureList container example commands These commands will use account_name as the name of the storage account To list all containers in your Azure storage account AzureList container -a account_name To confirm the container 191216-dar is present in your account AzureList container -a account_name 191216-dar To filter the list of containers to those starting with 19 AzureList container -a account_name 19* To filter the list of container to those starting with 19 and four additional digits followed by a dash AzureList container -a account_name 19d{4}-* To filter the list of containers to those starting with six digits, a dash, and three digits AzureList container -a account_name \\\\d{6}-\\\\D{3} To filter the list of containers to those ending with outputs AzureList container -a account_name *outputs\\$ To filter the list of containers to those that start with 19 and four additional digits, followed by a dash, three letters, and does not contain the word outputs AzureList container -a account_name 1912\\\\d{2}-\\\\D{3}\\(\\?\\!*output\\) AzureList container usage usage: AzureList container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE] [expression] Filter and list containers in your Azure storage account positional arguments: expression Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_FILE, --output_file OUTPUT_FILE Optionally provide the name and path of file in which the outputs are to be saved. AzureList search Filter files in a container (or containers) in Azure storage AzureList search required arguments account name AzureList search optional arguments container_name: name of the Azure storage container. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! output_file: name and path of file in which the outputs are to be saved. passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info AzureList search example commands These commands will use account_name as the name of the storage account. Note that all the regex examples used in AzureList container can be used here To list all files in all containers in your storage account AzureList search -a account_name To list all files in all containers ending with .gz AzureList search -a account_name \\*.gz To list all files in the container container-name AzureList search -a account_name -c container_name To list all files in the container container-name starting with reports AzureList search -a account_name -c container_name reports* To list all files in the container container-name ending with .gz AzureList search -a account_name -c container-name \\*.gz To list all files in the container container-name that contain .gz AzureList search -a account_name -c container-name \\*.gz* To list all files in the container container-name that contain .gz (but not at the end) AzureList search -a account_name -c container-name \\*.gz.+ AzureList search usage usage: AzureList search [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE] [-c [CONTAINER_NAME]] [expression] Filter files in a container (or containers) in Azure storage positional arguments: expression Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_FILE, --output_file OUTPUT_FILE Optionally provide the name and path of file in which the outputs are to be saved. -c [CONTAINER_NAME], --container_name [CONTAINER_NAME] Name of the Azure storage container. This command supports regular expressions e.g. 1912* will return all containers starting with 1912.Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! You can make your queries as complex as you wish: 1912\\d{2}-\\D{3}\\(\\?\\!*output\\) will only return containers that start with 1912, and have two additional digits. If the word output is present, any matches are ignored. There also have to be exactly three letters following a dash and the first six numbers e.g. 191216-dar and 191227-dar will be returned but not 191216-dar-outputs 191202-test, 191216dar, 1912162-dar, 191203-m05722, 191114-gta, or 200105-dar (and many others)","title":"List"},{"location":"list/#azurelist","text":"List and optionally filter containers and/or files in your Azure storage account Choose either the container , or the search functionality This script allows you to filter using regular expressions, so make sure you know what you're doing , check out a tutorial , look at a cheatsheet , and/or test your expressions Important: since the regular expressions are being entered on the command line, you will need to escape certain characters e.g. ! should be !","title":"AzureList"},{"location":"list/#general-usage","text":"usage: AzureList [-h] {container,search} ... Explore your Azure storage account optional arguments: -h, --help show this help message and exit Available functionality: {container,search} container Filter and list containers in your Azure storage account search Search files in a container (or containers) in Azure storage","title":"General Usage"},{"location":"list/#azurelist-container","text":"List and optionally filter containers in your Azure storage account","title":"AzureList container"},{"location":"list/#azurelist-container-required-arguments","text":"account name","title":"AzureList container required arguments"},{"location":"list/#azurelist-container-optional-arguments","text":"expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! output_file: name and path of file in which the outputs are to be saved. passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"AzureList container optional arguments"},{"location":"list/#azurelist-container-example-commands","text":"These commands will use account_name as the name of the storage account To list all containers in your Azure storage account AzureList container -a account_name To confirm the container 191216-dar is present in your account AzureList container -a account_name 191216-dar To filter the list of containers to those starting with 19 AzureList container -a account_name 19* To filter the list of container to those starting with 19 and four additional digits followed by a dash AzureList container -a account_name 19d{4}-* To filter the list of containers to those starting with six digits, a dash, and three digits AzureList container -a account_name \\\\d{6}-\\\\D{3} To filter the list of containers to those ending with outputs AzureList container -a account_name *outputs\\$ To filter the list of containers to those that start with 19 and four additional digits, followed by a dash, three letters, and does not contain the word outputs AzureList container -a account_name 1912\\\\d{2}-\\\\D{3}\\(\\?\\!*output\\)","title":"AzureList container example commands"},{"location":"list/#azurelist-container-usage","text":"usage: AzureList container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE] [expression] Filter and list containers in your Azure storage account positional arguments: expression Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_FILE, --output_file OUTPUT_FILE Optionally provide the name and path of file in which the outputs are to be saved.","title":"AzureList container usage"},{"location":"list/#azurelist-search","text":"Filter files in a container (or containers) in Azure storage","title":"AzureList search"},{"location":"list/#azurelist-search-required-arguments","text":"account name","title":"AzureList search required arguments"},{"location":"list/#azurelist-search-optional-arguments","text":"container_name: name of the Azure storage container. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! output_file: name and path of file in which the outputs are to be saved. passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"AzureList search optional arguments"},{"location":"list/#azurelist-search-example-commands","text":"These commands will use account_name as the name of the storage account. Note that all the regex examples used in AzureList container can be used here To list all files in all containers in your storage account AzureList search -a account_name To list all files in all containers ending with .gz AzureList search -a account_name \\*.gz To list all files in the container container-name AzureList search -a account_name -c container_name To list all files in the container container-name starting with reports AzureList search -a account_name -c container_name reports* To list all files in the container container-name ending with .gz AzureList search -a account_name -c container-name \\*.gz To list all files in the container container-name that contain .gz AzureList search -a account_name -c container-name \\*.gz* To list all files in the container container-name that contain .gz (but not at the end) AzureList search -a account_name -c container-name \\*.gz.+","title":"AzureList search example commands"},{"location":"list/#azurelist-search-usage","text":"usage: AzureList search [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE] [-c [CONTAINER_NAME]] [expression] Filter files in a container (or containers) in Azure storage positional arguments: expression Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! optional arguments: -h, --help show this help message and exit -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -o OUTPUT_FILE, --output_file OUTPUT_FILE Optionally provide the name and path of file in which the outputs are to be saved. -c [CONTAINER_NAME], --container_name [CONTAINER_NAME] Name of the Azure storage container. This command supports regular expressions e.g. 1912* will return all containers starting with 1912.Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\! You can make your queries as complex as you wish: 1912\\d{2}-\\D{3}\\(\\?\\!*output\\) will only return containers that start with 1912, and have two additional digits. If the word output is present, any matches are ignored. There also have to be exactly three letters following a dash and the first six numbers e.g. 191216-dar and 191227-dar will be returned but not 191216-dar-outputs 191202-test, 191216dar, 1912162-dar, 191203-m05722, 191114-gta, or 200105-dar (and many others)","title":"AzureList search usage"},{"location":"move/","text":"AzureMove Move containers, files, or folders within your Azure storage account. Choose either the container , file , or folder functionality General usage usage: AzureMove [-h] {container,file,folder} ... Move containers, files, or folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Move a container in Azure storage file Move a file within Azure storage folder Move a folder within Azure storage AzureMove container Move a container within your Azure storage account Required arguments: container name account name Optional arguments: target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot Example commands: These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To perform a basic move (this also renames a container): AzureMove container -a account_name -c container-name -t target-container To move a container, and set the storage tier to Cool AzureMove container -a account_name -c container-name -t target-container -s Cool To move a container and nest it into folder outputs : AzureMove container -a account_name -c container-name -t target-container -r outputs Usage usage: AzureMove container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] Move a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot AzureMove file Move a file within your Azure storage account Required arguments: container name account name file name Optional arguments: target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot Example commands: These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To move the file file_name.gz AzureMove file -a account_name -c container-name -t target-container -f file_name.gz To move the file file_name.gz , and set the storage tier to Cool AzureMove file -a account_name -c container-name -t target-container -f file_name.gz -s Cool To move the file file_name.gz nested in folder outputs AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz To move the file file_name.gz nested in folder outputs to the root of the source container AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r \"\" To move the file file_name.gz nested in folder outputs to folder results in the source container AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r results To move the file file_name.gz nested in folder outputs to the root of the target container AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r \"\" To move the file file_name.gz nested in folder outputs to folder results in the target container AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r results Usage usage: AzureMove file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] -f FILE Move a file within Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FILE, --file FILE Name of blob file to move in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz AzureMove folder Move a folder within your Azure storage account Required arguments: container name account name folder name Optional arguments: target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot Example commands: These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To move the folder folder_name AzureMove folder -a account_name -c container-name -t target-container -f folder_name To move the folder folder_name , and set the storage tier to Cool AzureMove folder -a account_name -c container-name -t target-container -f folder_name -s Cool To move the folder folder_name nested in folder outputs AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name To move the folder folder_name nested in folder outputs to the root of the source container AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r \"\" To move the folder folder_name nested in folder outputs to folder results in the source container AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r results To move the folder folder_name nested in folder outputs to the root of the target container AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r \"\" To move the folder folder_name nested in folder outputs to folder results in the target container AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r results Usage usage: AzureMove folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] -f FOLDER Move a folder within Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FOLDER, --folder FOLDER Name of folder to move in Azure storage. e.g. InterOp","title":"Move"},{"location":"move/#azuremove","text":"Move containers, files, or folders within your Azure storage account. Choose either the container , file , or folder functionality","title":"AzureMove"},{"location":"move/#general-usage","text":"usage: AzureMove [-h] {container,file,folder} ... Move containers, files, or folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Move a container in Azure storage file Move a file within Azure storage folder Move a folder within Azure storage","title":"General usage"},{"location":"move/#azuremove-container","text":"Move a container within your Azure storage account","title":"AzureMove container"},{"location":"move/#required-arguments","text":"container name account name","title":"Required arguments:"},{"location":"move/#optional-arguments","text":"target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot","title":"Optional arguments:"},{"location":"move/#example-commands","text":"These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To perform a basic move (this also renames a container): AzureMove container -a account_name -c container-name -t target-container To move a container, and set the storage tier to Cool AzureMove container -a account_name -c container-name -t target-container -s Cool To move a container and nest it into folder outputs : AzureMove container -a account_name -c container-name -t target-container -r outputs","title":"Example commands:"},{"location":"move/#usage","text":"usage: AzureMove container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] Move a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot","title":"Usage"},{"location":"move/#azuremove-file","text":"Move a file within your Azure storage account","title":"AzureMove file"},{"location":"move/#required-arguments_1","text":"container name account name file name","title":"Required arguments:"},{"location":"move/#optional-arguments_1","text":"target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot","title":"Optional arguments:"},{"location":"move/#example-commands_1","text":"These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To move the file file_name.gz AzureMove file -a account_name -c container-name -t target-container -f file_name.gz To move the file file_name.gz , and set the storage tier to Cool AzureMove file -a account_name -c container-name -t target-container -f file_name.gz -s Cool To move the file file_name.gz nested in folder outputs AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz To move the file file_name.gz nested in folder outputs to the root of the source container AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r \"\" To move the file file_name.gz nested in folder outputs to folder results in the source container AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r results To move the file file_name.gz nested in folder outputs to the root of the target container AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r \"\" To move the file file_name.gz nested in folder outputs to folder results in the target container AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r results","title":"Example commands:"},{"location":"move/#usage_1","text":"usage: AzureMove file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] -f FILE Move a file within Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FILE, --file FILE Name of blob file to move in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz","title":"Usage"},{"location":"move/#azuremove-folder","text":"Move a folder within your Azure storage account","title":"AzureMove folder"},{"location":"move/#required-arguments_2","text":"container name account name folder name","title":"Required arguments:"},{"location":"move/#optional-arguments_2","text":"target container: name of the container into which the container is to be moved path to store the container: nest the container within the target container passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot","title":"Optional arguments:"},{"location":"move/#example-commands_2","text":"These commands will use container-name as the name of the container, target-container as the name of the target container, and account_name as the name of the storage account To move the folder folder_name AzureMove folder -a account_name -c container-name -t target-container -f folder_name To move the folder folder_name , and set the storage tier to Cool AzureMove folder -a account_name -c container-name -t target-container -f folder_name -s Cool To move the folder folder_name nested in folder outputs AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name To move the folder folder_name nested in folder outputs to the root of the source container AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r \"\" To move the folder folder_name nested in folder outputs to folder results in the source container AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r results To move the folder folder_name nested in folder outputs to the root of the target container AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r \"\" To move the folder folder_name nested in folder outputs to folder results in the target container AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r results","title":"Example commands:"},{"location":"move/#usage_2","text":"usage: AzureMove folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH] [-s STORAGE_TIER] -f FOLDER Move a folder within Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -t TARGET_CONTAINER, --target_container TARGET_CONTAINER The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container -r RESET_PATH, --reset_path RESET_PATH Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or '' -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for the container/file/folder to be moved. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FOLDER, --folder FOLDER Name of folder to move in Azure storage. e.g. InterOp","title":"Usage"},{"location":"sas_url/","text":"AzureSAS Create shared access signatures (SAS) URLs for containers, files, folders in your Azure storage account. Note that each file in a container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS URLs will be provided Choose either the container , file , or folder functionality General usage usage: AzureSAS [-h] {container,file,folder} ... Create shared access signatures (SAS) for containers/files/folders from Azure storage. Note that each file in the container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS will be provided optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Create SAS for all files in a container in Azure storage file Create a SAS for a file in Azure storage folder Create SAS for all files in a folder in Azure storage AzureSAS container Create SAS URLs for all files in a container in your Azure storage account Required arguments: container name account name Optional arguments: output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container, and account_name as the name of the storage account To create SAS URLs with default settings: AzureSAS container -a account_name -c container-name To create SAS URLs with an expiry of 15 days: AzureSAS container -a account_name -c container-name -e 15 To create SAS URLs, and save them to the file sas_urls.txt in your current working directory: AzureSAS container -a account_name -c container-name -o sas_urls.txt To create SAS URLs, and save them to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS container -a account_name -c container-name -o outputs/sas_urls.txt Usage usage: AzureSAS container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] Create SAS URLs for all files in a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt AzureSAS file Create a SAS URL for a file in a container in your Azure storage account Required arguments: container name account name file name Optional arguments: output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container, and account_name as the name of the storage account To create a SAS URL for file file_name.gz with default settings: AzureSAS file -a account_name -c container-name -f file_name.gz To create a SAS URL for file file_name.gz nested in folder outputs with default settings: AzureSAS file -a account_name -c container-name -f outputs/file_name.gz To create a SAS URL for file file_name.gz with an expiry of 15 days: AzureSAS file -a account_name -c container-name f file_name.gz -e 15 To create a SAS URL for file file_name.gz , and save it to the file sas_urls.txt in your current working directory: AzureSAS file -a account_name -c container-name -f file_name.gz -o sas_urls.txt To create a SAS URL for file file_name.gz , and save it to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS file -a account_name -c container-name -f file_name.gz -o outputs/sas_urls.txt Usage usage: AzureSAS file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FILE Create a SAS URL for a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt -f FILE, --file FILE Path of file in Azure storage from which a SAS URL is to be created. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz AzureSAS folder Create SAS URLs for all files in a folder in your Azure storage account Required arguments: container name account name folder name Optional arguments: output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example commands: These commands will use container-name as the name of the container, and account_name as the name of the storage account To create SAS URLs for all files in folder folder_name with default settings: AzureSAS folder -a account_name -c container-name -f folder_name To create SAS URLs for all files in folder folder_name nested in folder outputs with default settings: AzureSAS folder -a account_name -c container-name -f outputs/folder_name To create SAS URLs for all files in folder folder_name with an expiry of 15 days: AzureSAS folder -a account_name -c container-name f folder_name -e 15 To create SAS URLs for all files in folder folder_name , and save them to the file sas_urls.txt in your current working directory: AzureSAS folder -a account_name -c container-name -f folder_name -o sas_urls.txt To create SAS URLs for all files in folder folder_name , and save them to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS folder -a account_name -c container-name -f folder_name -o outputs/sas_urls.txt Usage usage: AzureSAS folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FOLDER Create SAS URLs for all files in a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt -f FOLDER, --folder FOLDER Name of the folder for which SAS URLs are to be created for all files. e.g. InterOp","title":"SAS URL"},{"location":"sas_url/#azuresas","text":"Create shared access signatures (SAS) URLs for containers, files, folders in your Azure storage account. Note that each file in a container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS URLs will be provided Choose either the container , file , or folder functionality","title":"AzureSAS"},{"location":"sas_url/#general-usage","text":"usage: AzureSAS [-h] {container,file,folder} ... Create shared access signatures (SAS) for containers/files/folders from Azure storage. Note that each file in the container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS will be provided optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Create SAS for all files in a container in Azure storage file Create a SAS for a file in Azure storage folder Create SAS for all files in a folder in Azure storage","title":"General usage"},{"location":"sas_url/#azuresas-container","text":"Create SAS URLs for all files in a container in your Azure storage account","title":"AzureSAS container"},{"location":"sas_url/#required-arguments","text":"container name account name","title":"Required arguments:"},{"location":"sas_url/#optional-arguments","text":"output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"sas_url/#example-commands","text":"These commands will use container-name as the name of the container, and account_name as the name of the storage account To create SAS URLs with default settings: AzureSAS container -a account_name -c container-name To create SAS URLs with an expiry of 15 days: AzureSAS container -a account_name -c container-name -e 15 To create SAS URLs, and save them to the file sas_urls.txt in your current working directory: AzureSAS container -a account_name -c container-name -o sas_urls.txt To create SAS URLs, and save them to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS container -a account_name -c container-name -o outputs/sas_urls.txt","title":"Example commands:"},{"location":"sas_url/#usage","text":"usage: AzureSAS container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] Create SAS URLs for all files in a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt","title":"Usage"},{"location":"sas_url/#azuresas-file","text":"Create a SAS URL for a file in a container in your Azure storage account","title":"AzureSAS file"},{"location":"sas_url/#required-arguments_1","text":"container name account name file name","title":"Required arguments:"},{"location":"sas_url/#optional-arguments_1","text":"output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"sas_url/#example-commands_1","text":"These commands will use container-name as the name of the container, and account_name as the name of the storage account To create a SAS URL for file file_name.gz with default settings: AzureSAS file -a account_name -c container-name -f file_name.gz To create a SAS URL for file file_name.gz nested in folder outputs with default settings: AzureSAS file -a account_name -c container-name -f outputs/file_name.gz To create a SAS URL for file file_name.gz with an expiry of 15 days: AzureSAS file -a account_name -c container-name f file_name.gz -e 15 To create a SAS URL for file file_name.gz , and save it to the file sas_urls.txt in your current working directory: AzureSAS file -a account_name -c container-name -f file_name.gz -o sas_urls.txt To create a SAS URL for file file_name.gz , and save it to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS file -a account_name -c container-name -f file_name.gz -o outputs/sas_urls.txt","title":"Example commands:"},{"location":"sas_url/#usage_1","text":"usage: AzureSAS file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FILE Create a SAS URL for a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt -f FILE, --file FILE Path of file in Azure storage from which a SAS URL is to be created. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz","title":"Usage"},{"location":"sas_url/#azuresas-folder","text":"Create SAS URLs for all files in a folder in your Azure storage account","title":"AzureSAS folder"},{"location":"sas_url/#required-arguments_2","text":"container name account name folder name","title":"Required arguments:"},{"location":"sas_url/#optional-arguments_2","text":"output file: file in which the SAS URLs are to be written. Default is sas.txt in your current working directory expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10 passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"sas_url/#example-commands_2","text":"These commands will use container-name as the name of the container, and account_name as the name of the storage account To create SAS URLs for all files in folder folder_name with default settings: AzureSAS folder -a account_name -c container-name -f folder_name To create SAS URLs for all files in folder folder_name nested in folder outputs with default settings: AzureSAS folder -a account_name -c container-name -f outputs/folder_name To create SAS URLs for all files in folder folder_name with an expiry of 15 days: AzureSAS folder -a account_name -c container-name f folder_name -e 15 To create SAS URLs for all files in folder folder_name , and save them to the file sas_urls.txt in your current working directory: AzureSAS folder -a account_name -c container-name -f folder_name -o sas_urls.txt To create SAS URLs for all files in folder folder_name , and save them to the file sas_urls.txt nested in folder outputs in your current working directory: AzureSAS folder -a account_name -c container-name -f folder_name -o outputs/sas_urls.txt","title":"Example commands:"},{"location":"sas_url/#usage_2","text":"usage: AzureSAS folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FOLDER Create SAS URLs for all files in a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -e EXPIRY, --expiry EXPIRY The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10. -o OUTPUT_FILE, --output_file OUTPUT_FILE Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt -f FOLDER, --folder FOLDER Name of the folder for which SAS URLs are to be created for all files. e.g. InterOp","title":"Usage"},{"location":"set_tier/","text":"AzureTier Set the storage tier ( Hot , Cool , or Archive ) for containers, files, or folders in your Azure storage account Choose either the container , file , or folder functionality General usage usage: AzureTier [-h] {container,file,folder} ... Set the storage tier of containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Change the storage tier of a container in Azure storage file Change the storage tier of a file in Azure storage folder Change the storage tier of a folder in Azure storage AzureTier container Set the storage tier of a container in your Azure storage account Required arguments: container name account name storage tier Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example command: These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of a container to Cool AzureTier -a account_name -c container-name -s Cool Usage usage: AzureTier container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER Change the storage tier of a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\" AzureTier file Set the storage tier of a file in your Azure storage account Required arguments: container name account name file name storage tier Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example command: These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of the file file_name.gz to Archive AzureTier -a account_name -c container-name -f file_name.gz -s Archive Usage usage: AzureTier file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER -f FILE Change the storage tier of a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\" -f FILE, --file FILE Name of file in Azure storage that will have its storage tier sete.g. 220202-m05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz AzureTier folder Set the storage tier of a folder in your Azure storage account Required arguments: container name account name folder name storage tier Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info Example command: These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of the folder results/folder_name to Hot AzureTier -a account_name -c container-name -f results/folder_name -s Hot Usage usage: AzureTier folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER -f FOLDER Change the storage tier of a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\" -f FOLDER, --folder FOLDER Name of the folder in Azure storage that will have its storage tier set e.g. InterOp","title":"Set Tier"},{"location":"set_tier/#azuretier","text":"Set the storage tier ( Hot , Cool , or Archive ) for containers, files, or folders in your Azure storage account Choose either the container , file , or folder functionality","title":"AzureTier"},{"location":"set_tier/#general-usage","text":"usage: AzureTier [-h] {container,file,folder} ... Set the storage tier of containers/files/folders in Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {container,file,folder} container Change the storage tier of a container in Azure storage file Change the storage tier of a file in Azure storage folder Change the storage tier of a folder in Azure storage","title":"General usage"},{"location":"set_tier/#azuretier-container","text":"Set the storage tier of a container in your Azure storage account","title":"AzureTier container"},{"location":"set_tier/#required-arguments","text":"container name account name storage tier","title":"Required arguments:"},{"location":"set_tier/#optional-arguments","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"set_tier/#example-command","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of a container to Cool AzureTier -a account_name -c container-name -s Cool","title":"Example command:"},{"location":"set_tier/#usage","text":"usage: AzureTier container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER Change the storage tier of a container in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\"","title":"Usage"},{"location":"set_tier/#azuretier-file","text":"Set the storage tier of a file in your Azure storage account","title":"AzureTier file"},{"location":"set_tier/#required-arguments_1","text":"container name account name file name storage tier","title":"Required arguments:"},{"location":"set_tier/#optional-arguments_1","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"set_tier/#example-command_1","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of the file file_name.gz to Archive AzureTier -a account_name -c container-name -f file_name.gz -s Archive","title":"Example command:"},{"location":"set_tier/#usage_1","text":"usage: AzureTier file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER -f FILE Change the storage tier of a file in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\" -f FILE, --file FILE Name of file in Azure storage that will have its storage tier sete.g. 220202-m05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz","title":"Usage"},{"location":"set_tier/#azuretier-folder","text":"Set the storage tier of a folder in your Azure storage account","title":"AzureTier folder"},{"location":"set_tier/#required-arguments_2","text":"container name account name folder name storage tier","title":"Required arguments:"},{"location":"set_tier/#optional-arguments_2","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info","title":"Optional arguments:"},{"location":"set_tier/#example-command_2","text":"These commands will use container-name as the name of the container and account_name as the name of the storage account To change the storage tier of the folder results/folder_name to Hot AzureTier -a account_name -c container-name -f results/folder_name -s Hot","title":"Example command:"},{"location":"set_tier/#usage_2","text":"usage: AzureTier folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER -f FOLDER Change the storage tier of a folder in Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v VERBOSITY, --verbosity VERBOSITY Set the logging level. Options are debug, info, warning, error, and critical. Default is info. -s STORAGE_TIER, --storage_tier STORAGE_TIER Set the storage tier for a container/file/folder. Options are \"Hot\", \"Cool\", and \"Archive\" -f FOLDER, --folder FOLDER Name of the folder in Azure storage that will have its storage tier set e.g. InterOp","title":"Usage"},{"location":"upload/","text":"AzureUpload AzureUpload allows you to upload a file or a folder to your Azure storage account. Choose either the file or folder functionality General Usage usage: AzureUpload [-h] {file,folder} ... Upload files or folders to Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {file,folder} file Upload a file to Azure storage folder Upload a folder to Azure storage AzureUpload file Upload a single file to your Azure storage account. Required arguments: container name account name name and path of file to upload Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info path to store the file: change the folder structure of the file in Azure storage compared to your local system storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot Example commands: These commands will use container-name as the name of the container, and account_name as the name of the storage account To upload the file file_name.gz in your current working directory: AzureUpload file -a account_name -c container-name -f file_name.gz To upload the file file_name.gz in your current working directory and set the storage tier to Cool : AzureUpload file -a account_name -c container-name -f file_name.gz -s Cool To upload the file file_name.gz nested in the folder outputs in your current working directory: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz To upload the file file_name.gz nested in the folder outputs in your current working directory to the root of the container: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r \"\" To upload the file file_name.gz nested in the folder outputs in your current working directory to the folder results/parsing in the container: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r results/parsing To upload the file /home/users/account/files/file_name.gz to path data : AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r data To upload that same file to the root of the container: AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r \"\" To retain the path of the file: AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz Usage usage: AzureUpload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v {debug,info,warning,error,critical}] [-r RESET_PATH] [-s {Hot,Cool,Archive}] -f FILE Upload a file to Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical} Set the logging level. Default is info. -r RESET_PATH, --reset_path RESET_PATH Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use \"\" or '' -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive} Set the storage tier for the file/folder to be uploaded. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FILE, --file FILE Name and path of the file to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz AzureUpload folder Upload a single folder (and its contents) to your Azure storage account. Note that having a trailing slash ('/') at the end of your folder name will not affect the script Required arguments: container name account name name and path of folder to upload Optional arguments: passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info path to store the file: change the folder structure of the file in Azure storage compared to your local system storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot Example commands: These commands will use container-name as the name of the container, and account_name as the name of the storage account To upload the folder folder_name in your current working directory: AzureUpload folder -a account_name -c container-name -f folder_name To upload the folder folder_name in your current working directory and set the storage tier to Cool : AzureUpload folder -a account_name -c container-name -f folder_name -s Cool To upload the folder folder_name nested in the folder outputs in your current working directory: AzureUpload folder -a account_name -c container-name -f outputs/folder_name To upload the folder folder_name nested in the folder outputs in your current working directory to the root of the container: AzureUpload folder -a account_name -c container-name -f outputs/file_name.gz -r \"\" To upload the folder folder_name nested in the folder outputs in your current working directory to the folder results/parsing in the container: AzureUpload folder -a account_name -c container-name -f outputs/folder_namw -r results/parsing To upload the folder /home/users/account/files/ to path data : AzureUpload folder -a account_name -c container-name -f /home/users/account/files/ -r data To upload that same folder to the root of the container: AzureUpload folder -a account_name -c container-name -f /home/users/account/files -r \"\" To retain the path of the folder: AzureUpload folder -a account_name -c container-name -f /home/users/account/files/ Usage usage: AzureUpload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v {debug,info,warning,error,critical}] [-r RESET_PATH] [-s {Hot,Cool,Archive}] -f FOLDER Upload a folder to Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical} Set the logging level. Default is info. -r RESET_PATH, --reset_path RESET_PATH Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use \"\" or '' -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive} Set the storage tier for the file/folder to be uploaded. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FOLDER, --folder FOLDER Name and path of the folder to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/","title":"Upload"},{"location":"upload/#azureupload","text":"AzureUpload allows you to upload a file or a folder to your Azure storage account. Choose either the file or folder functionality","title":"AzureUpload"},{"location":"upload/#general-usage","text":"usage: AzureUpload [-h] {file,folder} ... Upload files or folders to Azure storage optional arguments: -h, --help show this help message and exit Available functionality: {file,folder} file Upload a file to Azure storage folder Upload a folder to Azure storage","title":"General Usage"},{"location":"upload/#azureupload-file","text":"Upload a single file to your Azure storage account.","title":"AzureUpload file"},{"location":"upload/#required-arguments","text":"container name account name name and path of file to upload","title":"Required arguments:"},{"location":"upload/#optional-arguments","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info path to store the file: change the folder structure of the file in Azure storage compared to your local system storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot","title":"Optional arguments:"},{"location":"upload/#example-commands","text":"These commands will use container-name as the name of the container, and account_name as the name of the storage account To upload the file file_name.gz in your current working directory: AzureUpload file -a account_name -c container-name -f file_name.gz To upload the file file_name.gz in your current working directory and set the storage tier to Cool : AzureUpload file -a account_name -c container-name -f file_name.gz -s Cool To upload the file file_name.gz nested in the folder outputs in your current working directory: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz To upload the file file_name.gz nested in the folder outputs in your current working directory to the root of the container: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r \"\" To upload the file file_name.gz nested in the folder outputs in your current working directory to the folder results/parsing in the container: AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r results/parsing To upload the file /home/users/account/files/file_name.gz to path data : AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r data To upload that same file to the root of the container: AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r \"\" To retain the path of the file: AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz","title":"Example commands:"},{"location":"upload/#usage","text":"usage: AzureUpload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v {debug,info,warning,error,critical}] [-r RESET_PATH] [-s {Hot,Cool,Archive}] -f FILE Upload a file to Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical} Set the logging level. Default is info. -r RESET_PATH, --reset_path RESET_PATH Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use \"\" or '' -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive} Set the storage tier for the file/folder to be uploaded. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FILE, --file FILE Name and path of the file to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz","title":"Usage"},{"location":"upload/#azureupload-folder","text":"Upload a single folder (and its contents) to your Azure storage account. Note that having a trailing slash ('/') at the end of your folder name will not affect the script","title":"AzureUpload folder"},{"location":"upload/#required-arguments_1","text":"container name account name name and path of folder to upload","title":"Required arguments:"},{"location":"upload/#optional-arguments_1","text":"passphrase used to store your connection string in the system keyring (default is AzureStorage) verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info path to store the file: change the folder structure of the file in Azure storage compared to your local system storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot","title":"Optional arguments:"},{"location":"upload/#example-commands_1","text":"These commands will use container-name as the name of the container, and account_name as the name of the storage account To upload the folder folder_name in your current working directory: AzureUpload folder -a account_name -c container-name -f folder_name To upload the folder folder_name in your current working directory and set the storage tier to Cool : AzureUpload folder -a account_name -c container-name -f folder_name -s Cool To upload the folder folder_name nested in the folder outputs in your current working directory: AzureUpload folder -a account_name -c container-name -f outputs/folder_name To upload the folder folder_name nested in the folder outputs in your current working directory to the root of the container: AzureUpload folder -a account_name -c container-name -f outputs/file_name.gz -r \"\" To upload the folder folder_name nested in the folder outputs in your current working directory to the folder results/parsing in the container: AzureUpload folder -a account_name -c container-name -f outputs/folder_namw -r results/parsing To upload the folder /home/users/account/files/ to path data : AzureUpload folder -a account_name -c container-name -f /home/users/account/files/ -r data To upload that same folder to the root of the container: AzureUpload folder -a account_name -c container-name -f /home/users/account/files -r \"\" To retain the path of the folder: AzureUpload folder -a account_name -c container-name -f /home/users/account/files/","title":"Example commands:"},{"location":"upload/#usage_1","text":"usage: AzureUpload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v {debug,info,warning,error,critical}] [-r RESET_PATH] [-s {Hot,Cool,Archive}] -f FOLDER Upload a folder to Azure storage optional arguments: -h, --help show this help message and exit -c CONTAINER_NAME, --container_name CONTAINER_NAME Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted. -a ACCOUNT_NAME, --account_name ACCOUNT_NAME Name of the Azure storage account -p PASSPHRASE, --passphrase PASSPHRASE The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is \"AzureStorage\". -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical} Set the logging level. Default is info. -r RESET_PATH, --reset_path RESET_PATH Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use \"\" or '' -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive} Set the storage tier for the file/folder to be uploaded. Options are \"Hot\", \"Cool\", and \"Archive\". Default is Hot -f FOLDER, --folder FOLDER Name and path of the folder to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/","title":"Usage"}]}
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