From 4d97e9d1b70754eeb1689d497c298adff538bac4 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 May 2026 13:27:32 +0200 Subject: [PATCH 1/6] Add cowsay --- .../2025.06/eessi-2025.06-eb-5.3.0-001-system.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml index 446ebf605a..c6e9800048 100644 --- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml +++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml @@ -1,2 +1,3 @@ easyconfigs: - Julia-1.12.2.eb + - cowsay-3.04.eb From 6ddd9c99fff8c1ec47d10cdcbd3dcbef1865f51d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 May 2026 14:59:58 +0200 Subject: [PATCH 2/6] Add samtools --- .../software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml index 944e924f78..e3b932df62 100644 --- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml +++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml @@ -12,3 +12,4 @@ easyconfigs: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/24956 from-commit: a3bb54895c3de5600fdfd2893a818378daebc7ee + - SAMtools-1.22.1-GCC-14.3.0.eb From feaa2553e664a7550471bc4ac060d4d1a4f7c4a2 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 May 2026 15:00:15 +0200 Subject: [PATCH 3/6] Remove cowsay --- .../2025.06/eessi-2025.06-eb-5.3.0-001-system.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml index c6e9800048..446ebf605a 100644 --- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml +++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml @@ -1,3 +1,2 @@ easyconfigs: - Julia-1.12.2.eb - - cowsay-3.04.eb From f063d44b02a856a96b77310626e3c1a870dd7192 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 May 2026 15:26:57 +0200 Subject: [PATCH 4/6] Replace Samtools with biopython --- .../software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml index e3b932df62..e50da6c337 100644 --- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml +++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml @@ -12,4 +12,4 @@ easyconfigs: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/24956 from-commit: a3bb54895c3de5600fdfd2893a818378daebc7ee - - SAMtools-1.22.1-GCC-14.3.0.eb + - Biopython-1.86-gfbf-2025b.eb From e48ebd2a0da998e90f3825ac3ee76b074fef4e67 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 18 May 2026 14:18:56 +0200 Subject: [PATCH 5/6] Use feature branch from our own software-layer-scripts to see if we can get site builds to work --- bot/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bot/build.sh b/bot/build.sh index 2884db8de4..2a560bae0c 100755 --- a/bot/build.sh +++ b/bot/build.sh @@ -3,7 +3,7 @@ # give up as soon as any error occurs set -e -git clone https://github.com/EESSI/software-layer-scripts +git clone -b improve_building_on_top_support https://github.com/SURF-hpcv/software-layer-scripts # symlink everything, except for: # - common files like LICENSE and README.md From 0038ca8e14a98d8c941eda4eea71bed434960903 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 26 May 2026 16:01:46 +0200 Subject: [PATCH 6/6] Apply suggestions from code review Co-authored-by: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> --- .../software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml index 5bee0681ec..a35075b1db 100644 --- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml +++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml @@ -12,9 +12,7 @@ easyconfigs: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/24956 from-commit: a3bb54895c3de5600fdfd2893a818378daebc7ee -<<<<<<< add_cowsay2 - Biopython-1.86-gfbf-2025b.eb -======= - Extrae-5.0.0-gompi-2025b.eb: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/25798 @@ -32,4 +30,3 @@ easyconfigs: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/25999 from-commit: 960bb9bbf98f11ac376f43a3d36d5cf1cedc96f1 - QuantumESPRESSO-7.5-foss-2025b.eb ->>>>>>> main