From b9f784ca8ddd2b8d9bda9d7ede03e0623c6dc992 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:27:58 +0200
Subject: [PATCH 1/4] {2023.06}[foss/2022a] add common dependencies - set 1

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 86dcd7714a..b1bbe71da7 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,3 +5,6 @@ easyconfigs:
   - 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
+  - gzip-1.12-GCCcore-11.3.0.eb
+  - lz4-1.9.3-GCCcore-11.3.0.eb
+  - zstd-1.5.2-GCCcore-11.3.0.eb

From f8265a14f57b220a38c9faf1c7b049fb401e0db3 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:36:36 +0200
Subject: [PATCH 2/4] add Java to set

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

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index b1bbe71da7..f8caa95a54 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,6 +5,8 @@ easyconfigs:
   - 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
+  # wraps around Java/11.0.20
+  - Java-11.eb
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb

From f0b5fda7edcaaae28bb37d10546ae5112b6348ab Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:43:04 +0200
Subject: [PATCH 3/4] move Java to stack file for system toolchain

---
 .github/workflows/test_eessi.yml  | 1 +
 eessi-2023.06-eb-4.8.1-2022a.yml  | 2 --
 eessi-2023.06-eb-4.8.1-system.yml | 3 +++
 3 files changed, 4 insertions(+), 2 deletions(-)
 create mode 100644 eessi-2023.06-eb-4.8.1-system.yml

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 832d4cf74f..64269d2982 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -26,6 +26,7 @@ jobs:
         - 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
+        - eessi-2023.06-eb-4.8.1-system.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index f8caa95a54..b1bbe71da7 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,8 +5,6 @@ easyconfigs:
   - 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
-  # wraps around Java/11.0.20
-  - Java-11.eb
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
diff --git a/eessi-2023.06-eb-4.8.1-system.yml b/eessi-2023.06-eb-4.8.1-system.yml
new file mode 100644
index 0000000000..fb3f7af4cb
--- /dev/null
+++ b/eessi-2023.06-eb-4.8.1-system.yml
@@ -0,0 +1,3 @@
+easyconfigs:
+  # wraps around Java/11.0.20
+  - Java-11.eb

From 3fc94ed6ac3889c3d0f5afe19a89bcb4ac867732 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 19:49:04 +0200
Subject: [PATCH 4/4] filter out .modulerc.lua (for Java) in create_tarball.sh,
 see EESSI/software-layer PR-327

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index b6c72b341d..65f6efc2dc 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -52,7 +52,7 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type l | grep -v '/\.wh\.' >> ${files_list}
     # module files and symlinks
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules/all -type f -o -type l \
-        | grep -v '/\.wh\.' | sed -e 's/.lua$//' | sed -e 's@.*/modules/all/@@g' | sort -u \
+        | grep -v '/\.wh\.' | grep -v '/\.modulerc\.lua' | sed -e 's/.lua$//' | sed -e 's@.*/modules/all/@@g' | sort -u \
         >> ${module_files_list}
 fi
 if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software -a -r ${module_files_list} ]; then