From 448f0ab05440c4904a64cf5b83d9f340f349f54c Mon Sep 17 00:00:00 2001 From: Richard Top Date: Mon, 5 Aug 2024 06:52:05 +0000 Subject: [PATCH 1/4] {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 --- .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml | 1 + .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml | 1 + eb_hooks.py | 11 +++++++++++ 3 files changed, 13 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml index 7a04eaa9d3..27a79d8c80 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml @@ -1,2 +1,3 @@ easyconfigs: - BLAST+-2.14.0-gompi-2022b.eb + - BioPerl-1.7.8-GCCcore-12.2.0.eb diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml index 90dda5236b..e60cd83909 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml @@ -30,3 +30,4 @@ easyconfigs: - librosa-0.10.1-foss-2023a.eb - xarray-2023.9.0-gfbf-2023a.eb - SciTools-Iris-3.9.0-foss-2023a.eb + - BioPerl-1.7.8-GCCcore-12.3.0.eb diff --git a/eb_hooks.py b/eb_hooks.py index 7f7e4e57bd..eafcb5b417 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -647,6 +647,16 @@ def post_sanitycheck_hook(self, *args, **kwargs): POST_SANITYCHECK_HOOKS[self.name](self, *args, **kwargs) +def post_sanitycheck_bioperl(self, *args, **kwargs): + """ + Allow the copy of easyblock perlmodule.py to /tmp/eb... after sanity check by changing directory permissions + """ + if self.name == 'BioPerl': + print_msg("Adding user write permission for EasyBuild directories under /tmp/eb*...") + bioperlcmd = "chmod u+w -R /tmp/eb*" + run_cmd(bioperlcmd) + + def post_sanitycheck_cuda(self, *args, **kwargs): """ Remove files from CUDA installation that we are not allowed to ship, @@ -791,5 +801,6 @@ def inject_gpu_property(ec): } POST_SANITYCHECK_HOOKS = { + 'BioPerl': post_sanitycheck_bioperl, 'CUDA': post_sanitycheck_cuda, } From 4b37ea27c969fea88211761141238e4f65b90872 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Mon, 5 Aug 2024 12:42:33 +0000 Subject: [PATCH 2/4] removed BioPerl hook --- eb_hooks.py | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/eb_hooks.py b/eb_hooks.py index eafcb5b417..7f7e4e57bd 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -647,16 +647,6 @@ def post_sanitycheck_hook(self, *args, **kwargs): POST_SANITYCHECK_HOOKS[self.name](self, *args, **kwargs) -def post_sanitycheck_bioperl(self, *args, **kwargs): - """ - Allow the copy of easyblock perlmodule.py to /tmp/eb... after sanity check by changing directory permissions - """ - if self.name == 'BioPerl': - print_msg("Adding user write permission for EasyBuild directories under /tmp/eb*...") - bioperlcmd = "chmod u+w -R /tmp/eb*" - run_cmd(bioperlcmd) - - def post_sanitycheck_cuda(self, *args, **kwargs): """ Remove files from CUDA installation that we are not allowed to ship, @@ -801,6 +791,5 @@ def inject_gpu_property(ec): } POST_SANITYCHECK_HOOKS = { - 'BioPerl': post_sanitycheck_bioperl, 'CUDA': post_sanitycheck_cuda, } From e194d2a88a2b38879ac816a392ff77c145480583 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Tue, 6 Aug 2024 11:28:00 +0000 Subject: [PATCH 3/4] Added --include-easyblock and an issue reference to EasyBuild framework --- .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml | 5 ++++- .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml index 27a79d8c80..1c4ea68b3f 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml @@ -1,3 +1,6 @@ easyconfigs: - BLAST+-2.14.0-gompi-2022b.eb - - BioPerl-1.7.8-GCCcore-12.2.0.eb + - BioPerl-1.7.8-GCCcore-12.2.0.eb: + options: + # see https://github.com/easybuilders/easybuild-framework/issues/4602 + include-easyblocks-from-commit: 89ea2e4737d792055de828e18f38bccee26b76cf diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml index e60cd83909..a5b425dc09 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml @@ -30,4 +30,7 @@ easyconfigs: - librosa-0.10.1-foss-2023a.eb - xarray-2023.9.0-gfbf-2023a.eb - SciTools-Iris-3.9.0-foss-2023a.eb - - BioPerl-1.7.8-GCCcore-12.3.0.eb + - BioPerl-1.7.8-GCCcore-12.3.0.eb: + options: + # see https://github.com/easybuilders/easybuild-framework/issues/4602 + include-easyblocks-from-commit: 89ea2e4737d792055de828e18f38bccee26b76cf From 448e6b30c47dbea249c0ed6f89880ed229f3e659 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 6 Aug 2024 16:16:59 +0200 Subject: [PATCH 4/4] Apply suggestions from code review --- .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml | 4 ++-- .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml index 1c4ea68b3f..140876f43b 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml @@ -2,5 +2,5 @@ easyconfigs: - BLAST+-2.14.0-gompi-2022b.eb - BioPerl-1.7.8-GCCcore-12.2.0.eb: options: - # see https://github.com/easybuilders/easybuild-framework/issues/4602 - include-easyblocks-from-commit: 89ea2e4737d792055de828e18f38bccee26b76cf + # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21136 + from-commit: d8076ebaf8cb915762adebf88d385cc672b350dc diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml index 14dc2a17bc..e07ed409a4 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml @@ -38,5 +38,5 @@ easyconfigs: from-commit: f0e91e6e430ebf902f7788ebb47f0203dee60649 - BioPerl-1.7.8-GCCcore-12.3.0.eb: options: - # see https://github.com/easybuilders/easybuild-framework/issues/4602 - include-easyblocks-from-commit: 89ea2e4737d792055de828e18f38bccee26b76cf + # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21136 + from-commit: d8076ebaf8cb915762adebf88d385cc672b350dc