From e9ca7ed29fa95df92f1d7f0f3921f110ea227c65 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Thu, 24 Oct 2024 17:10:41 -0400 Subject: [PATCH] fix mount instructions for micromamba --- docs/contributors.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/contributors.rst b/docs/contributors.rst index 47f46327..92241a78 100644 --- a/docs/contributors.rst +++ b/docs/contributors.rst @@ -23,13 +23,13 @@ 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 \ + -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/ @@ -37,14 +37,14 @@ 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 \ + -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 Singularity analogous to ``docker`` using the ``--bind`` (``-B``) option: :: $ singularity run \ - -B $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep \ + -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/