Final?

.github/workflows/tools_install.sh

@@ -11,3 +11,21 @@ python $TOOLDIR/get-pip.py --force-reinstall
 # All MATLAB tools MUST be installed referred by the parameterset
 source $GITHUB_WORKSPACE/.github/workflows/tools_urls.sh
 source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_tools.sh $GITHUB_WORKSPACE/.github/workflows/$PARAMETER_XML $TOOLDIR
+
+echo "FSL: ${LOAD_FSL}; FREESURFER: ${LOAD_FREESURFER}"
+
+if [[ "x${LOAD_FSL}x" == "x1x" ]]; then
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 0 $TOOLDIR/config/fsl_bash.sh
+else # FSL standards are needed for some modules
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 1
+fi
+
+if [[ "x${LOAD_FREESURFER}x" == "x1x" ]]; then
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_freesurfer.sh $TOOLDIR 7.2.0 centos7 "[email protected]\n7061\n *Ccpi6x7PAIeQ\n FS96pPK5vW.0g" $TEMPLATEDIR
+fi
+
+echo "Free space:"
+df -h
+mkdir $HOME/.aa
+cp $GITHUB_WORKSPACE/.github/workflows/$PARAMETER_XML $HOME/.aa/aap_parameters_user.xml
+mkdir $HOME/projects

.github/workflows/trigger_install.py

@@ -1,6 +1,7 @@
 # Note: Assume Python 2.7, since that will have been installed for facemasking requirements.
 #
-# Using python (instead of matlab) because using system() in matlab gives enormous amount of command window output.
+# Using python (instead of matlab) because using system() in matlab gives enormous amount of
+# command window output, and there is some problem with the status code from system()
 
 import sys
 import subprocess
@@ -16,29 +17,6 @@
     print("Your system is Linux")
     sys.stdout.flush()
     subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/tools_install.sh', shell=True, executable="/bin/bash")
-    #if status<0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running tools_install')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
-
-    subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/tools_install_b.sh', shell=True, executable="/bin/bash")
-    #if status!=0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running tools_install_b')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
-
-    # Configure aa
-    subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/configure_aa.sh', shell=True, executable="/bin/bash")
-    #if status!=0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running configure_aa')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
 
 elif plt == "Darwin":
     print("Your system is MacOS")