Needed to set PATH for fs_install_mcr to work

maouw · Dec 27, 2023 · 7938a1d · 7938a1d
1 parent 7a33894
commit 7938a1d
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/def/hyakvnc-freesurfer-ubuntu22.04/Singularity b/def/hyakvnc-freesurfer-ubuntu22.04/Singularity
@@ -54,10 +54,15 @@ 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 Matlab Compiler Runtime (MCR) if requested:
+  if [ -n "{{MCR_VERSION}}" ]; then
     # Install MCR dependencies:
     apt-get install -y libxt-dev libxext-dev libncurses5
 
+		# Set the environment variables for fs_install_mcr to work:
+		export FREESURFER_HOME="/usr/local/freesurfer/{{FREESURFER_VERSION}}"
+		export PATH="${FREESURFER_HOME}/bin:${PATH}"
+
     # Install MCR:
     fs_install_mcr "{{MCR_VERSION}}"
   fi
@@ -80,7 +85,7 @@ This is an Apptainer container of Ubuntu 22.04 with FreeSurfer installed. It is
 	export MNI_DATAPATH="${FREESURFER_HOME}/mni/data"
 	export PERL5LIB="${MINC_LIB_DIR}/perl5/5.8.5"
 	export MNI_PERL5LIB="${MINC_LIB_DIR}/perl5/5.8.5"
-	export PATH="${FREESURFER_HOME}/bin:${FREESURFER_HOME}/tktools:${MINC_BIN_DIR}:$PATH"
+	export PATH="${FREESURFER_HOME}/bin:${FREESURFER_HOME}/tktools:${MINC_BIN_DIR}:${PATH}"
 	export FS_LICENSE="${FS_LICENSE:-${HOME}/${USER}/.freesurfer_license.txt}"
 
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