Skip to content

Commit

Permalink
chore(build): Install Workbench CLI via conda (#3410)
Browse files Browse the repository at this point in the history
I got connectome-workbench onto conda-forge:
https://github.com/conda-forge/connectome-workbench-split-feedstock

It has a connectome-workbench-cli package that excludes the GUI, and now
this is one fewer things to have special in the Dockerfile.
  • Loading branch information
effigies authored Dec 17, 2024
2 parents 152a80d + a0d44bf commit cf360a3
Show file tree
Hide file tree
Showing 2 changed files with 2 additions and 14 deletions.
14 changes: 0 additions & 14 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -77,15 +77,6 @@ RUN mkdir -p /opt/afni-latest \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete

# Connectome Workbench 1.5.0
FROM downloader AS workbench
RUN mkdir /opt/workbench && \
curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
unzip workbench-linux64-v1.5.0.zip -d /opt && \
rm workbench-linux64-v1.5.0.zip && \
rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5

# Micromamba
FROM downloader AS micromamba

Expand Down Expand Up @@ -174,7 +165,6 @@ RUN apt-get update -qq \
# Install files from stages
COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=workbench /opt/workbench /opt/workbench

# Simulate SetUpFreeSurfer.sh
ENV OS="Linux" \
Expand All @@ -198,10 +188,6 @@ ENV PATH="/opt/afni-latest:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_PLUGINPATH="/opt/afni-latest"

# Workbench config
ENV PATH="/opt/workbench/bin_linux64:$PATH" \
LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users fmriprep
WORKDIR /home/fmriprep
Expand Down
2 changes: 2 additions & 0 deletions env.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@ dependencies:
- ants=2.5
# Workflow dependencies: Convert3d
- convert3d=1.4
# Workflow dependencies: Connectome Workbench
- connectome-workbench-cli=2.0
# Workflow dependencies: FSL (versions pinned in 6.0.7.13)
- fsl-bet2=2111.8
- fsl-flirt=2111.2
Expand Down

0 comments on commit cf360a3

Please sign in to comment.