diff --git a/Dockerfile b/Dockerfile index 117c684dc..334a0e544 100644 --- a/Dockerfile +++ b/Dockerfile @@ -88,6 +88,15 @@ 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 \ + --exclude "c3d-1.4.0-Linux-x86_64/lib" \ + --exclude "c3d-1.4.0-Linux-x86_64/share" \ + --exclude "c3d-1.4.0-Linux-x86_64/bin/c3d_gui" + # Micromamba FROM downloader as micromamba WORKDIR / @@ -168,6 +177,7 @@ 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 /opt/convert3d # Simulate SetUpFreeSurfer.sh ENV OS="Linux" \ diff --git a/env.yml b/env.yml index 8c5229d70..5f10d520a 100644 --- a/env.yml +++ b/env.yml @@ -23,9 +23,6 @@ dependencies: # Utilities - graphviz=6.0 - pandoc=3.1 - # Workflow dependencies: Convert3D - - convert3d=1.3.0 - - libitk=5.2 # 5.3 fails with c3d # Workflow dependencies: ANTs - ants=2.4.4 # Workflow dependencies: FSL (versions pinned in 6.0.6.2)