Bundling Matlab MCR into base freesurfer image

maouw · Dec 27, 2023 · 395fe68 · 395fe68
1 parent 1f3f0ea
commit 395fe68
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Showing 3 changed files with 9 additions and 37 deletions.
diff --git a/.github/workflows/apptainer-image.yml b/.github/workflows/apptainer-image.yml
@@ -130,12 +130,11 @@ jobs:
     - name: Build Container
       run: |
         set -euxo pipefail
-        export APPTAINER_CACHE_DIR="${SETUP_DOWNLOADS_DIR}/apptainer-cache"
         mkdir -p sif
         pushd  "${DEF_DIR}"
         echo "Building \"${IMAGE_NAME}.sif\""
         touch .build-arg-file
-        apptainer build --warn-unused-build-args --fix-perms --force --build-arg-file .build-arg-file ../../sif/"${IMAGE_NAME}.sif" Singularity || { echo "Failed to build \"${IMAGE_NAME}.sif\""; exit 1; }
+        apptainer build --warn-unused-build-args --disable-cache --fix-perms --force --build-arg-file .build-arg-file ../../sif/"${IMAGE_NAME}.sif" Singularity || { echo "Failed to build \"${IMAGE_NAME}.sif\""; exit 1; }
         echo "Built \"${IMAGE_NAME}.sif\""
         popd
     - name: Login and Deploy Container

diff --git a/def/hyakvnc-freesurfer-matlab-ubuntu22.04/Singularity b/def/hyakvnc-freesurfer-matlab-ubuntu22.04/Singularity
diff --git a/def/hyakvnc-freesurfer-ubuntu22.04/Singularity b/def/hyakvnc-freesurfer-ubuntu22.04/Singularity
@@ -12,6 +12,7 @@ From: {{BOOTSTRAP_FROM_REPO}}/{{BOOTSTRAP_FROM_IMAGE}}{{BOOTSTRAP_FROM_SUFFIX}}
 	SETUP_DOWNLOADS_DIR=../../.setup-downloads
 	RECON_ALL_CLINICAL_HASH=ecdf46e
 	RECON_ALL_CLINICAL_URL=https://raw.githubusercontent.com/freesurfer/freesurfer/{{RECON_ALL_CLINICAL_HASH}}/recon_all_clinical/recon-all-clinical.sh
+  MCR_VERSION=R2014b
 
 %help
 This is an Apptainer container of Ubuntu 22.04 with FreeSurfer installed. It is designed to be run on the Hyak cluster at the University of Washington with the hyakvnc script.
@@ -53,6 +54,13 @@ This is an Apptainer container of Ubuntu 22.04 with FreeSurfer installed. It is
 		"{{RECON_ALL_CLINICAL_URL}}" || { echo "warning: curl failed!" >&2; exit 1; }
 	chmod a+x /usr/local/freesurfer/{{FREESURFER_VERSION}}/bin/recon-all-clinical.sh
 
+  if [[ -n "{{ MCR_VERSION }}" ]; then
+    # Install MCR dependencies:
+    apt-get install -y libxt-dev libxext-dev libncurses5
+
+    # Install MCR:
+    fs_install_mcr "{{MCR_VERSION}}"
+  fi
 	# Clean up packages:
 	apt-get clean -y -qq && apt-get -y autoremove && rm -rf /var/lib/apt/lists/*
 
@@ -81,4 +89,3 @@ This is an Apptainer container of Ubuntu 22.04 with FreeSurfer installed. It is
 	edu.uw.hyakvnc.container.resources.recommends.cpus 4
 	edu.uw.hyakvnc.container.resources.requires.cpus 1
 	edu.uw.hyakvnc.container.resources.suggests.gpus 1
-