From a0d44bf93d2f91dff21ddbb6a6cadb93528da7bb Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 26 Nov 2024 10:12:43 -0500 Subject: [PATCH] chore(build): Install Workbench CLI via conda --- Dockerfile | 14 -------------- env.yml | 2 ++ 2 files changed, 2 insertions(+), 14 deletions(-) diff --git a/Dockerfile b/Dockerfile index 37f85d7a..ed4c594a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 @@ -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" \ @@ -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 diff --git a/env.yml b/env.yml index d680f3a6..2defb977 100644 --- a/env.yml +++ b/env.yml @@ -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