From 0aa927951bce99caf6e68f222082ded09f381256 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Oct 2023 19:57:22 +0200
Subject: [PATCH 1/2] determine easystack files to process via PR patch file

---
 EESSI-pilot-install-software.sh | 50 ++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 22 deletions(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index ed5319a6db..db8d0d99cd 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -41,7 +41,7 @@ function copy_build_log() {
         echo "- working directory: ${PWD}" >> ${build_log_path}
         echo "- Slurm job ID: ${SLURM_OUT}" >> ${build_log_path}
         echo "- EasyBuild version: ${eb_version}" >> ${build_log_path}
-        echo "- easystack file: ${es}" >> ${build_log_path}
+        echo "- easystack file: ${easystack_file}" >> ${build_log_path}
 
         echo "EasyBuild log file ${build_log} copied to ${build_log_path} (with context appended)"
     fi
@@ -186,36 +186,42 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-for eb_version in '4.7.2' '4.8.0' '4.8.1'; do
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# use PR patch file to determine in which easystack files stuff was added
+for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$'); do
+
+    echo "Processing easystack file ${easystack_file}...\n\n"
+
+    # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+    eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
 
     # load EasyBuild module (will be installed if it's not available yet)
     source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
 
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
 
-    for es in $(ls eessi-${EESSI_PILOT_VERSION}-eb-${eb_version}-*.yml); do
-
-        if [ -f ${es} ]; then
-            echo_green "Feeding easystack file ${es} to EasyBuild..."
+    if [ -f ${easystack_file} ]; then
+        echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 
-            ${EB} --easystack ${TOPDIR}/${es} --robot
-            ec=$?
+        ${EB} --easystack ${TOPDIR}/${easystack_file} --robot
+        ec=$?
 
-            # copy EasyBuild log file if EasyBuild exited with an error
-            if [ ${ec} -ne 0 ]; then
-                eb_last_log=$(unset EB_VERBOSE; eb --last-log)
-                # copy to current working directory
-                cp -a ${eb_last_log} .
-                echo "Last EasyBuild log file copied from ${eb_last_log} to ${PWD}"
-                # copy to build logs dir (with context added)
-                copy_build_log "${eb_last_log}" "${build_logs_dir}"
-            fi
-
-            $TOPDIR/check_missing_installations.sh ${TOPDIR}/${es}
-        else
-            fatal_error "Easystack file ${es} not found!"
+        # copy EasyBuild log file if EasyBuild exited with an error
+        if [ ${ec} -ne 0 ]; then
+            eb_last_log=$(unset EB_VERBOSE; eb --last-log)
+            # copy to current working directory
+            cp -a ${eb_last_log} .
+            echo "Last EasyBuild log file copied from ${eb_last_log} to ${PWD}"
+            # copy to build logs dir (with context added)
+            copy_build_log "${eb_last_log}" "${build_logs_dir}"
         fi
-    done
+
+        $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file}
+    else
+        fatal_error "Easystack file ${easystack_file} not found!"
+    fi
 
 done
 

From 890d98675d03db9443b20175cdd2e001051291ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Oct 2023 20:41:34 +0200
Subject: [PATCH 2/2] add Bowtie

---
 eessi-2023.06-eb-4.7.2-2022a.yml | 1 +
 eessi-2023.06-eb-4.8.1-2023a.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/eessi-2023.06-eb-4.7.2-2022a.yml b/eessi-2023.06-eb-4.7.2-2022a.yml
index d40ddff261..6bb86a1b76 100644
--- a/eessi-2023.06-eb-4.7.2-2022a.yml
+++ b/eessi-2023.06-eb-4.7.2-2022a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - GCC-11.3.0
   - OpenMPI-4.1.4-GCC-11.3.0.eb
+  - Bowtie2-2.4.5-GCC-11.3.0.eb
diff --git a/eessi-2023.06-eb-4.8.1-2023a.yml b/eessi-2023.06-eb-4.8.1-2023a.yml
index b015676757..def264c0bc 100644
--- a/eessi-2023.06-eb-4.8.1-2023a.yml
+++ b/eessi-2023.06-eb-4.8.1-2023a.yml
@@ -8,3 +8,4 @@ easyconfigs:
       options:
         from-pr: 18887
   - foss-2023a
+  - Bowtie2-2.5.1-GCC-12.3.0