fnndsc/pl-multipass repository overview

multipass
        [--exec <appToRun>]                                         \
        [--specificArgs <specificArgs>]                             \
        [--splitExpr <splitOn>]                                     \
        [--commonArgs <commonArgs>]                                 \
        [-h] [--help]                                               \
        [--json]                                                    \
        [--man]                                                     \
        [--meta]                                                    \
        [--savejson <DIR>]                                          \
        [--noJobLogging]                                            \
        [--verbose <level>]                                         \
        [--version]                                                 \
        <inputDir>                                                  \
        <outputDir>

.. code::

        [--exec <appToRun>]
        A specific ``app`` to run in _multi-phase_ mode. This app must by
        necessity exist within the  ``multiphase`` container. See the
        ``requirements.txt`` for list of installed apps

        [--specificArgs <specificArgs>]
        This is a string list of per-phase specific arguments. Each
        phase is separated by <splitOn> expression.

        [--splitExpr <splitOn>]
        The expression on which to split the <specificArgs> string.
        Default is '++'.

        [--commonArgs <commonArgs>]
        This is a raw string of args, common to each phase call of the
        <appToRun>.

        [-h] [--help]
        If specified, show help message and exit.

        [--json]
        If specified, show json representation of app and exit.

        [--man]
        If specified, print (this) man page and exit.

        [--meta]
        If specified, print plugin meta data and exit.

        [--savejson <DIR>]
        If specified, save json representation file to DIR and exit.

        [--noJobLogging]
        Turns off per-job logging to file system.

        [--verbose <level>]
        Verbosity level for app: 0->silent, 5->talkative.

        [--version]
        If specified, print version number and exit.


Getting inline help is:

.. code:: bash

    docker run --rm fnndsc/pl-multipass multipass --man

Run
~~~

You need you need to specify input and output directories using the `-v` flag to `docker run`.


.. code:: bash

    docker run --rm -u $(id -u)                                     \
        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing              \
        fnndsc/pl-multipass multipass                               \
        /incoming /outgoing


Development
-----------

Build the Docker container:

.. code:: bash

    docker build -t local/pl-multipass .


Debug
-----

To debug the containerized version of this plugin, simply volume map the source directories of the repo into the relevant locations of the container image:

.. code:: bash

    docker run -ti --rm -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw        \
        -v $PWD/multipass:/usr/local/lib/python3.9/site-packages/multipass:ro   \
        fnndsc/pl-multipass multipass /incoming /outgoing

To enter the container:

.. code:: bash

    docker run -ti --rm -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw        \
        -v $PWD/multipass:/usr/local/lib/python3.9/site-packages/multipass:ro   \
        --entrypoint /bin/bash fnndsc/pl-multipass

Remember to use the ``-ti`` flag for interactivity! Volume mapping the original host source directory in the above example is optional.


*30*

.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
    :target: https://chrisstore.co