Metadata-Version: 1.1
Name: msgen
Version: 0.6.15
Summary: Microsoft Genomics Command-line Client
Home-page: UNKNOWN
Author: Microsoft Corporation, Microsoft Genomics Team
Author-email: msgensupp@microsoft.com
License: MIT
Description: msgen
        ========
        Microsoft Genomics Command-line Client
        
        Installation
        ------------
        `msgen`_ is on PyPI and can be installed via:
        
        Linux
        
        ::
        
          sudo apt-get install -y build-essential libssl-dev libffi-dev libpython-dev python-dev python-pip
          sudo pip install --upgrade --no-deps msgen
          sudo pip install msgen
        
        Windows
        
        ::
        
          pip install --upgrade --no-deps msgen
          pip install msgen
        
        
        msgen is compatible with Python 2.7. If you do not want to install msgen
        as a system-wide binary and modify system-wide python packages, use the
        ``--user`` flag with ``pip``.
        
        - Base Requirements
        
          - `azure-storage`_
          - `requests`_
        
        
        You can install these packages using pip, easy_install or through standard
        setup.py procedures. These dependencies will be automatically installed if
        using a package-based install or setup.py. The required versions of these
        dependent packages can be found in ``setup.py``.
        
        .. _azure-storage: https://pypi.python.org/pypi/azure-storage
        .. _requests: https://pypi.python.org/pypi/requests
        
        
        Release Notes
        -------------
        
        1. Ability to specify SAS token duration for input blobs and an output container. The default token duration is 24 hours.
        2. Ability to provide a short description for submitted workflows.
        3. Minor fixes and improvements.
        
        Usage
        -------------
        
        After installing msgen, a simple command to check connectivity is:
        
        ::
        
          msgen ^
            -api_url_base     https://malibutest0044.azure-api.net ^
            -subscription_key <MsGen_Subscription_Key>  ^
            -command          LIST
        
        ..
        
          Note: the ``^`` at the end of the lines above is a continuation character for this document and is not part of the command. On Linux, the continuation character is ``\``.
        
        You can get a full list of available arguments by running ``msgen -h``, but generally you will need to provide
        at least ``-api_url_base``, ``-subscription_key``, and ``-command``, where the value of ``-command`` is one of the following:
        
        =========  =====
        LIST       Returns a list of jobs you have submitted. Takes no arguments.
        SUBMIT     Submits a workflow request to the service. Needs at least ``-process_name`` and storage-related arguments. ``-process_name`` identifies the specific processing workflow and version to run.  Use ``snapgatk`` to run the latest process. To lock on a specific processing package you can use the explicit name, e.g. ``snapgatk-20170124_4``.
        GETSTATUS  Returns the status of the workflow specified by ``-workflow_id``.
        CANCEL     Sends a request to cancel processing of the workflow specified by ``-workflow_id``.
        =========  =====
        
        So, here is what a command to submit two fastq.gz files for processing may look like:
        
        ::
        
          msgen ^
            -api_url_base     https://malibutest0044.azure-api.net ^
            -subscription_key <MsGen_Subscription_Key> ^
            -command          SUBMIT ^
            -process_name     snapgatk ^
            -process_args     R=grch37bwa ^
            -description      <short_description>
            -input_storage_account_type       AZURE_BLOCK_BLOB ^
            -input_storage_account_name       <your_sa_name_in> ^
            -input_storage_account_key        <your_sa_key_in> ^
            -input_storage_account_container  <your_sa_container_name> ^
            -input_blob_name_1                <your_blob_reads_1> ^
            -input_blob_name_2                <your_blob_reads_2> ^
            -output_storage_account_type      AZURE_BLOCK_BLOB ^
            -output_storage_account_name      <your_sa_name_out> ^
            -output_storage_account_key       <your_sa_key_in> ^
            -output_storage_account_container <your_results_container> ^
            -output_filename_base             <your_results_basename>
            -sas_duration                     <sas_token_duration_in_hours>
        
        All of these arguments could be read from a configuration file which is included using the ``-f`` option:
        
        ::
        
          msgen -f sample.001.txt
        
        An example sample.001.txt configuration file that matches the above submit command would look like:
        
        ::
        
          # Microsoft Genomics Service - Command Line Interface - Configuration File
          # Instructions
          # 1.  Entries are provided in key-value pairs, like key:value
          # 2.  Whitespace (tabs, spaces) don't matter
          # 3.  Lines starting with # are ignored
          
          api_url_base:    https://malibutest0044.azure-api.net
          subscription_key: <MsGen_Subscription_Key>
          command:          SUBMIT
          process_name:     snapgatk
          process_args:     R=grch37bwa
          description:      <short_description>
          sas_duration:     <sas_token_duration_in_hours>
        
          input_storage_account_type:       AZURE_BLOCK_BLOB
          input_storage_account_name:       <your_sa_name_in>
          input_storage_account_key:        <your_sa_key_in>
          input_storage_account_container:  <your_sa_container_name>
          input_blob_name_1:                <your_blob_reads_1>
          input_blob_name_2:                <your_blob_reads_2>
          
          output_storage_account_type:      AZURE_BLOCK_BLOB
          output_storage_account_name:      <your_sa_name_out>
          output_storage_account_key:       <your_sa_key_in>
          output_storage_account_container: <your_results_container>
          output_filename_base:             <your_results_basename>
          output_overwrite:                 False
        
        When using the ``-f`` option, you may have arguments in the file, on the command line, or in both places.
        Any arguments you have on the command line will override a value found in the configuration file.
        
        ::
        
          msgen -f sample.001.txt -output_overwrite true -sas_duration 48
Keywords: azure genomics
Platform: any
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
