fnndsc/pl-mri10yr06mo01da_normal
Anonymized reference MRI
5.9K
.. 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
This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.
.. code::
mri10yr06mo01da_normal.python \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
[--dir <dir>] \
[--splash <splash>] \
<outputDir>
.. 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.
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
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
docker pull fnndsc/pl-mri10yr06mo01da_normal