From 2275b899b3f1c2c49b3bcf17f75167c83aa51f01 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sat, 12 Oct 2024 13:57:18 -0400 Subject: [PATCH 1/2] Remove c3d from Dockerfilr --- Dockerfile | 7 ------- 1 file changed, 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 10828c96..37f85d7a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -86,12 +86,6 @@ RUN mkdir /opt/workbench && \ 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 @@ -181,7 +175,6 @@ RUN apt-get update -qq \ 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" \ From 74a52985923a001afa92dae861f6e0550f535212 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sat, 12 Oct 2024 14:00:09 -0400 Subject: [PATCH 2/2] Add convert3d to env.yml --- env.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/env.yml b/env.yml index f6227e90..d680f3a6 100644 --- a/env.yml +++ b/env.yml @@ -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