Metadata-Version: 1.0
Name: mri10yr06mo01da_normal
Version: 1.1.2
Summary: An anonymized MRI exemplar
Home-page: https://github.com/FNNDSC/pl-mri10yr06mo01da_normal
Author: Rudolph Pienaar
Author-email: rudolph.pienaar@gmail.com
License: MIT
Description: pl-mri10yr06mo01da_normal
        ================================
        
        .. image:: https://badge.fury.io/py/mri10yr06mo01da_normal.svg
            :target: https://badge.fury.io/py/mri10yr06mo01da_normal
        
        .. image:: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal.svg?branch=master
            :target: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal
        
        .. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
            :target: https://badge.fury.io/py/pl-mri10yr06mo01da_normal
        
        .. contents:: Table of Contents
        
        
        Abstract
        --------
        
        This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.
        
        Synopsis
        --------
        
        .. code::
        
            mri10yr06mo01da_normal.python                                   \
                [-v <level>] [--verbosity <level>]                          \
                [--version]                                                 \
                [--man]                                                     \
                [--meta]                                                    \
                [--dir <dir>]                                               \
                [--splash <splash>]                                         \
                <outputDir>
        
        Arguments
        ---------
        
        .. code::
        
            [-v <level>] [--verbosity <level>]
            Verbosity level for app. Not used currently.
        
            [--version]
            If specified, print version number.
        
            [--man]
            If specified, print this man page.
        
            [--meta]
            If specified, print plugin meta data.
        
            [--splash <splash>]
            An optional splash message to print on startup.
        
            [--dir <dir>]
            An optional override directory to copy to the <outputDir>.
            Note, if run from a containerized version, this will copy 
            a directory from the *container* file system.
        
        Run
        ----
        
        This ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image.
        
        Using PyPI
        ~~~~~~~~~~
        
        To run from PyPI, simply do a 
        
        .. code:: bash
        
            pip install mri10yr06mo01da_normal
        
        and run with
        
        .. code:: bash
        
            mri10yr06mo01da_normal.py --man /tmp
        
        to get inline help. The app should also understand being called with only one positional argument
        
        .. code:: bash
        
            mri10yr06mo01da_normal.py /destination/directory
        
        Using ``docker run``
        ~~~~~~~~~~~~~~~~~~~~
        
        To run using ``docker``, be sure to assign an "input" directory to ``/incoming`` and an output directory to ``/outgoing``. *Make sure that the* ``$(pwd)/out`` *directory is world writable!*
        
        Now, prefix all calls with 
        
        .. code:: bash
        
            docker run --rm -v $(pwd)/out:/outgoing                             \
                    fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py                        \
        
        Thus, getting inline help is:
        
        .. code:: bash
        
            mkdir out && chmod 777 out
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
                    fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
                    --man                                                       \
                    /outgoing
        
        Examples
        --------
        
        Copy the embedded MRI data to the ``out`` directory
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
            mkdir out && chmod 777 out
            docker run --rm -v $(pwd)/out:/outgoing                             \
                    fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
                    /outgoing
        
        Copy a user specified directory to the ``out`` directory
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
            mkdir out && chmod 777 out
            docker run --rm -v $(pwd)/out:/outgoing                             \
                    fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
                    --dir /usr/src/data
                    /outgoing
        
        
        
        
        
Platform: UNKNOWN
