From 395fe6845576f92e16cf139badfd4e64e28a4696 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 26 Dec 2023 17:38:48 -0800
Subject: [PATCH] Bundling Matlab MCR into base freesurfer image

---
 .github/workflows/apptainer-image.yml         |  3 +-
 .../Singularity                               | 34 -------------------
 .../Singularity                               |  9 ++++-
 3 files changed, 9 insertions(+), 37 deletions(-)
 delete mode 100644 def/hyakvnc-freesurfer-matlab-ubuntu22.04/Singularity

diff --git a/.github/workflows/apptainer-image.yml b/.github/workflows/apptainer-image.yml
index a63d8e3..ce07713 100644
--- 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
deleted file mode 100644
index 4fe1652..0000000
--- a/def/hyakvnc-freesurfer-matlab-ubuntu22.04/Singularity
+++ /dev/null
@@ -1,34 +0,0 @@
-Bootstrap: {{BOOTSTRAP_SOURCE}}
-From: {{BOOTSTRAP_FROM_REPO}}/{{BOOTSTRAP_FROM_IMAGE}}{{BOOTSTRAP_FROM_SUFFIX}}
-
-%arguments
-	BOOTSTRAP_SOURCE=localimage
-	BOOTSTRAP_FROM_REPO=../../sif
-	BOOTSTRAP_FROM_IMAGE=hyakvnc-freesurfer-ubuntu22.04
-	BOOTSTRAP_FROM_SUFFIX=.sif
-	SETUP_DOWNLOADS_DIR=../../.setup-downloads
-  MCR_VERSION=R2014b
-  APT_CLEANUP=1
-
-%help
-	This is an Apptainer container of Ubuntu 22.04 with Matlab runtimes installed on top of the hyakvnc-freesurfer-ubuntu22.04 container.
-
-%setup
-	[ -n "${APPTAINER_ROOTFS:-}" ] && ../../bin/write-apptainer-labels.sh > "${APPTAINER_ROOTFS}/.build_labels"
-
-%post
-	set -eux
-	export DEBIAN_FRONTEND=noninteractive
-  APT_CLEANUP="{{APT_CLEANUP}}"
-
-	# Update the package list:
-	apt-get update -y -qq
-
-  # Install MCR dependencies:
-  apt-get install -y libxt-dev libxext-dev libncurses5
-
-  # Install MCR:
-  fs_install_mcr "{{MCR_VERSION}}"
-
-  # Clean up packages:
-  [ "${APT_CLEANUP:-0}" = 1 ] && apt-get clean -y -qq && rm -rf /var/lib/apt/lists/*
diff --git a/def/hyakvnc-freesurfer-ubuntu22.04/Singularity b/def/hyakvnc-freesurfer-ubuntu22.04/Singularity
index 1fdc686..214fb20 100644
--- 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
-