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fix mount instructions for micromamba #895

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fix mount instructions for micromamba
mattcieslak Oct 24, 2024
a5a17d3
Merge branch 'master' into doc/fix-mount-micromamba
mattcieslak Dec 3, 2024
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16 changes: 8 additions & 8 deletions docs/contributors.rst
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Expand Up @@ -25,28 +25,28 @@ container.
When invoking ``docker`` directly, the mount options must be specified
with the ``-v`` flag::

-v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro
-v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.10/site-packages/nipype:ro
-v $HOME/projects/qsiprep/qsiprep:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep:ro
-v $HOME/projects/nipype/nipype:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype:ro

For example, ::

$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
-v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro \
pennlinc/qsiprep:latest /data /out/out participant \
-v $HOME/projects/qsiprep/qsiprep:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep:ro \
pennbbl/qsiprep:latest /data /out/out participant \
-w /out/work/

In order to work directly in the container, use ``--entrypoint=bash``
arguments in a ``docker`` command::

$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
-v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro --entrypoint=bash \
pennlinc/qsiprep:latest
-v $HOME/projects/qsiprep/qsiprep:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep:ro --entrypoint=bash \
pennbbl/qsiprep:latest

Patching containers can be achieved in Apptainer analogous to ``docker``
using the ``--bind`` (``-B``) option: ::

$ apptainer run \
-B $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep \
$ singularity run \
-B $HOME/projects/qsiprep/qsiprep:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep \
qsiprep.img \
/scratch/dataset /scratch/out participant -w /out/work/

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