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                <h2 id="azureupload">AzureUpload</h2>
<p>AzureUpload allows you to upload a file or a folder to your Azure storage account.</p>
<p>Choose either the <a href="#azureupload-file"><code>file</code></a> or <a href="#azureupload-folder"><code>folder</code></a> functionality</p>
<h4 id="general-usage">General Usage</h4>
<pre><code>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
</code></pre>

<h3 id="azureupload-file">AzureUpload file</h3>
<p>Upload a single file to your Azure storage account. </p>
<h4 id="required-arguments">Required arguments:</h4>
<ul>
<li>container name</li>
<li>account name</li>
<li>name and path of file to upload</li>
</ul>
<h4 id="optional-arguments">Optional arguments:</h4>
<ul>
<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
<li>path to store the file: change the folder structure of the file in Azure storage compared to your local system</li>
<li>storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot</li>
</ul>
<h4 id="example-commands">Example commands:</h4>
<p>These commands will use <code>container-name</code> as the name of the container, and <code>account_name</code> as the name of the storage account</p>
<p>To upload the file <code>file_name.gz</code> in your current working directory:</p>
<p><code>AzureUpload file -a account_name -c container-name -f file_name.gz</code></p>
<p>To upload the file <code>file_name.gz</code> in your current working directory and set the storage tier to <code>Cool</code>:</p>
<p><code>AzureUpload file -a account_name -c container-name -f file_name.gz -s Cool</code></p>
<p>To upload the file <code>file_name.gz</code> nested in the folder <code>outputs</code> in your current working directory:</p>
<p><code>AzureUpload file -a account_name -c container-name -f outputs/file_name.gz</code></p>
<p>To upload the file <code>file_name.gz</code> nested in the folder <code>outputs</code> in your current working directory to the root of the container:</p>
<p><code>AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r ""</code></p>
<p>To upload the file <code>file_name.gz</code> nested in the folder <code>outputs</code> in your current working directory to the folder <code>results/parsing</code> in the container:</p>
<p><code>AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r results/parsing</code></p>
<p>To upload the file <code>/home/users/account/files/file_name.gz</code> to path <code>data</code>:</p>
<p><code>AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r data</code></p>
<p>To upload that same file to the root of the container:</p>
<p><code>AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r ""</code></p>
<p>To retain the path of the file:</p>
<p><code>AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz</code></p>
<h4 id="usage">Usage</h4>
<pre><code>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 &quot;AzureStorage&quot;.
  -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 &quot;&quot; or ''
  -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive}
                        Set the storage tier for the file/folder to be uploaded. Options are &quot;Hot&quot;, &quot;Cool&quot;, and &quot;Archive&quot;. 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
</code></pre>

<h3 id="azureupload-folder">AzureUpload folder</h3>
<p>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</p>
<h4 id="required-arguments_1">Required arguments:</h4>
<ul>
<li>container name</li>
<li>account name</li>
<li>name and path of folder to upload</li>
</ul>
<h4 id="optional-arguments_1">Optional arguments:</h4>
<ul>
<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
<li>path to store the file: change the folder structure of the file in Azure storage compared to your local system</li>
<li>storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot</li>
</ul>
<h4 id="example-commands_1">Example commands:</h4>
<p>These commands will use <code>container-name</code> as the name of the container, and <code>account_name</code> as the name of the storage account</p>
<p>To upload the folder <code>folder_name</code> in your current working directory:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f folder_name</code></p>
<p>To upload the folder <code>folder_name</code> in your current working directory and set the storage tier to <code>Cool</code>:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f folder_name -s Cool</code></p>
<p>To upload the folder <code>folder_name</code> nested in the folder <code>outputs</code> in your current working directory:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f outputs/folder_name</code></p>
<p>To upload the folder <code>folder_name</code> nested in the folder <code>outputs</code> in your current working directory to the root of the container:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f outputs/file_name.gz -r ""</code></p>
<p>To upload the folder <code>folder_name</code> nested in the folder <code>outputs</code> in your current working directory to the folder <code>results/parsing</code> in the container:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f outputs/folder_namw -r results/parsing</code></p>
<p>To upload the folder <code>/home/users/account/files/</code> to path <code>data</code>:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f /home/users/account/files/ -r data</code></p>
<p>To upload that same folder to the root of the container:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f /home/users/account/files -r ""</code></p>
<p>To retain the path of the folder:</p>
<p><code>AzureUpload folder -a account_name -c container-name -f /home/users/account/files/</code></p>
<h4 id="usage_1">Usage</h4>
<pre><code>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 &quot;AzureStorage&quot;.
  -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 &quot;&quot; or ''
  -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive}
                        Set the storage tier for the file/folder to be uploaded. Options are &quot;Hot&quot;, &quot;Cool&quot;, and &quot;Archive&quot;. Default is Hot
  -f FOLDER, --folder FOLDER
                        Name and path of the folder to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/

</code></pre>
              
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