diff --git a/docs/contributors.rst b/docs/contributors.rst index 2d62bf4c..1cdbf19f 100644 --- a/docs/contributors.rst +++ b/docs/contributors.rst @@ -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/