Merge pull request EESSI#179 from trz42/nessi-23.06-add-bio-packages-1

{2023.06}[foss/2022a] bio packages - set 1
trz42 · Oct 6, 2023 · b95d8c7 · b95d8c7
2 parents 646495d + 7cd9277
commit b95d8c7
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Showing 4 changed files with 41 additions and 13 deletions.
diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
@@ -4,14 +4,14 @@ on: [push, pull_request, workflow_dispatch]
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
-  eessi_pilot_repo:
+  pilot:
     runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
         EESSI_VERSION:
         - 2023.06
-        EESSI_SOFTWARE_SUBDIR_OVERRIDE:
+        EESSI_SOFTWARE_SUBDIR:
         - aarch64/generic
         - x86_64/amd/zen2
         - x86_64/intel/broadwell
@@ -25,6 +25,7 @@ jobs:
         - eessi-2023.06-eb-4.7.2-2022b.yml
         - eessi-2023.06-eb-4.7.2-system.yml
         - eessi-2023.06-eb-4.8.0-system.yml
+        - eessi-2023.06-eb-4.8.1-2022a.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
@@ -36,38 +37,55 @@ jobs:
               cvmfs_http_proxy: DIRECT
               cvmfs_repositories: pilot.nessi.no
 
-        - name: Test check_missing_installations.sh script
+        - name: Test check_missing_installations.sh script with EESSI_SOFTWARE_SUBDIR_OVERRIDE
+          if: '!cancelled()'
+          run: |
+              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR}}
+              source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
+              module load EasyBuild
+              eb --version
+              export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_OS_TYPE=linux
+              env | grep ^EESSI | sort
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
+              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
+
+        - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE
+          if: '!cancelled()'
           run: |
-              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
-              which eb
               eb --version
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
               ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
+          if: '!cancelled()'
           run: |
-              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               which eb
               eb --version
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              echo "modify easystack file by adding a missing package (GCC/8.3.0)"
-              echo "  - GCC-8.3.0:" >> ${{matrix.EASYSTACK_FILE}}
-              tail -n 5 ${{matrix.EASYSTACK_FILE}}
+              # create dummy easystack file with a single entry (something that is not installed in EESSI)
+              easystack_file="test.yml"
+              echo "easyconfigs:" > ${easystack_file}
+              echo "  - GCC-8.3.0:" >> ${easystack_file}
+              echo "created easystack file '${easystack_file}' with a missing installation (GCC/8.3.0):"
+              cat ${easystack_file}
               # note, check_missing_installations.sh exits 1 if a package was
               # missing, which is intepreted as false (exit code based, not
               # boolean logic), hence when the script exits 0 if no package was
               # missing it is interpreted as true, thus the test did not capture
               # the missing package
-              if ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}; then
+              if ./check_missing_installations.sh ${easystack_file}; then
                 echo "did NOT capture missing package; test FAILED"
                 exit 1
               else

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
@@ -172,8 +172,6 @@ if [ ! -z "${shared_fs_path}" ]; then
     export EASYBUILD_SOURCEPATH=${shared_eb_sourcepath}:${EASYBUILD_SOURCEPATH}
 fi
 
-${EB} --show-config
-
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
 module --force purge
@@ -200,6 +198,8 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
     # load EasyBuild module (will be installed if it's not available yet)
     source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
 
+    ${EB} --show-config
+
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
 
     if [ -f ${easystack_file} ]; then

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
@@ -22,6 +22,9 @@ source $TOPDIR/scripts/utils.sh
 
 source $TOPDIR/configure_easybuild
 
+echo ">> Active EasyBuild configuration when checking for missing installations:"
+${EB:-eb} --show-config
+
 echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..."
 eb_missing_out=$LOCAL_TMPDIR/eb_missing.out
 ${EB:-eb} --easystack ${easystack} --missing 2>&1 | tee ${eb_missing_out}

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -0,0 +1,7 @@
+easyconfigs:
+  - BAMM-2.5.0-foss-2022a.eb
+  - BamTools-2.5.2-GCC-11.3.0.eb
+  - BCFtools-1.15.1-GCC-11.3.0.eb
+  - Bowtie2-2.4.5-GCC-11.3.0.eb
+  - FastTree-2.1.11-GCCcore-11.3.0.eb
+  - SAMtools-1.16.1-GCC-11.3.0.eb