@@ -45,14 +45,14 @@ Note the ``-i`` flag allows you to specify an image.
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When invoking ``docker `` directly, the mount options must be specified
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with the ``-v `` flag::
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- -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6 /site-packages/fmriprep:ro
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- -v $HOME/projects/niworkflows/niworkflows:/usr/local/miniconda/lib/python3.6 /site-packages/niworkflows:ro
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- -v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.6 /site-packages/nipype:ro
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+ -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7 /site-packages/fmriprep:ro
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+ -v $HOME/projects/niworkflows/niworkflows:/usr/local/miniconda/lib/python3.7 /site-packages/niworkflows:ro
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+ -v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.7 /site-packages/nipype:ro
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For example, ::
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$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
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- -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6 /site-packages/fmriprep:ro \
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+ -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7 /site-packages/fmriprep:ro \
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poldracklab/fmriprep:latest /data /out/out participant \
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-w /out/work/
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@@ -65,14 +65,14 @@ This is the equivalent of using ``--entrypoint=bash`` and omitting the fmriprep
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arguments in a ``docker `` command::
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$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
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- -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6 /site-packages/fmriprep:ro --entrypoint=bash \
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+ -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7 /site-packages/fmriprep:ro --entrypoint=bash \
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poldracklab/fmriprep:latest
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Patching containers can be achieved in Singularity analogous to ``docker ``
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using the ``--bind `` (``-B ``) option: ::
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$ singularity run \
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- -B $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6 /site-packages/fmriprep \
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+ -B $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7 /site-packages/fmriprep \
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fmriprep.img \
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/scratch/dataset /scratch/out participant -w /out/work/
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