Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Install c3d through conda #3382

Merged
merged 2 commits into from
Oct 12, 2024
Merged

Install c3d through conda #3382

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2275b89
Remove c3d from Dockerfilr
effigies Oct 12, 2024
74a5298
Add convert3d to env.yml
effigies Oct 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 0 additions & 7 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,12 +86,6 @@
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

# Convert3d 1.4.0
FROM downloader AS c3d
RUN mkdir /opt/convert3d && \
curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Experimental/c3d-1.4.0-Linux-gcc64.tar.gz/download \
| tar -xz -C /opt/convert3d --strip-components 1

# Micromamba
FROM downloader AS micromamba

Expand Down Expand Up @@ -181,7 +175,6 @@
COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=workbench /opt/workbench /opt/workbench
COPY --from=c3d /opt/convert3d/bin/c3d_affine_tool /usr/bin/c3d_affine_tool

# Simulate SetUpFreeSurfer.sh
ENV OS="Linux" \
Expand All @@ -206,7 +199,7 @@
AFNI_PLUGINPATH="/opt/afni-latest"

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

Check warning on line 202 in Dockerfile

View workflow job for this annotation

GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$LD_LIBRARY_PATH'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"

# Create a shared $HOME directory
Expand All @@ -221,7 +214,7 @@
ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate fmriprep" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" \

Check warning on line 217 in Dockerfile

View workflow job for this annotation

GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$CPATH' (did you mean $PATH?)
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
CPATH="/opt/conda/envs/fmriprep/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/envs/fmriprep/lib:$LD_LIBRARY_PATH"

Expand Down
2 changes: 2 additions & 0 deletions env.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@ dependencies:
- pandoc=3.1
# Workflow dependencies: ANTs
- ants=2.5
# Workflow dependencies: Convert3d
- convert3d=1.4
# Workflow dependencies: FSL (versions pinned in 6.0.7.13)
- fsl-bet2=2111.8
- fsl-flirt=2111.2
Expand Down