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Update README
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rudolphpienaar committed Feb 5, 2021
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26 changes: 25 additions & 1 deletion README.rst
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Expand Up @@ -200,7 +200,7 @@ 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!*

- Make sure your current working directory is ``devel``. At this juncture it should contain `mgz_converter_dataset``.
- Make sure your current working directory is ``devel``. At this juncture it should contain ``mgz_converter_dataset``.

- Create an output directory named ``results`` in ``devel``.

Expand Down Expand Up @@ -237,6 +237,30 @@ Copy and modify the different commands below as needed:
/incoming /outgoing
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/mgz2imageslices:/usr/local/lib/python3.8/dist-packages/mgz2imageslices:ro \
fnndsc/pl-mgz2imageslices mgz2imageslices /incoming /outgoing
To enter the container:

.. code:: bash
docker run -ti --rm -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw \
-v $PWD/mgz2imageslices:/usr/local/lib/python3.8/dist-packages/mgz2imageslices:ro \
--entrypoint /bin/bash fnndsc/pl-mgz2imageslices
Remember to use the ``-ti`` flag for interactivity!


*30*




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