{bio}[gompi/2024a] HMMER v3.4

[ThomasHoffmann77]

(created using eb --new-pr)
from PR #21864

[github-actions]

Updated software HMMER-3.4-gompi-2024a.eb

Diff against HMMER-3.4-gompi-2023b.eb

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
index bb76dc1e93..5e40c90494 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -5,6 +5,7 @@
 # Authors::   Nils Christian <nils.christian@uni.lu>,
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
 # License::   MIT/GPL
 # $Id$
 #
@@ -29,7 +30,7 @@ description = """HMMER is used for searching sequence databases for homologs
  past, this strength came at significant computational expense, but in the new
  HMMER3 project, HMMER is now essentially as fast as BLAST."""
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = [
     'http://eddylab.org/software/hmmer/',
@@ -39,8 +40,8 @@ sources = [SOURCELOWER_TAR_GZ]
 checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
 
 builddependencies = [
-    ('Python', '3.11.5'),
-    ('Perl', '5.38.0'),
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
 ]
 
 # replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files

Diff against HMMER-3.4-gompi-2023a.eb

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
index 99f585d998..5e40c90494 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -5,6 +5,7 @@
 # Authors::   Nils Christian <nils.christian@uni.lu>,
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
 # License::   MIT/GPL
 # $Id$
 #
@@ -29,7 +30,7 @@ description = """HMMER is used for searching sequence databases for homologs
  past, this strength came at significant computational expense, but in the new
  HMMER3 project, HMMER is now essentially as fast as BLAST."""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = [
     'http://eddylab.org/software/hmmer/',
@@ -39,8 +40,8 @@ sources = [SOURCELOWER_TAR_GZ]
 checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
 
 builddependencies = [
-    ('Python', '3.11.3'),
-    ('Perl', '5.36.1'),
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
 ]
 
 # replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files

Diff against HMMER-3.3.2-gompi-2022b.eb

easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
index e5a79c3da2..5e40c90494 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -5,6 +5,7 @@
 # Authors::   Nils Christian <nils.christian@uni.lu>,
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
 # License::   MIT/GPL
 # $Id$
 #
@@ -16,7 +17,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'HMMER'
-version = '3.3.2'
+version = '3.4'
 
 homepage = 'http://hmmer.org/'
 description = """HMMER is used for searching sequence databases for homologs
@@ -29,24 +30,23 @@ description = """HMMER is used for searching sequence databases for homologs
  past, this strength came at significant computational expense, but in the new
  HMMER3 project, HMMER is now essentially as fast as BLAST."""
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = [
     'http://eddylab.org/software/hmmer/',
     'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-patches = ['%(name)s-%(version)s_fix_perl.patch']
-checksums = [
-    {'hmmer-3.3.2.tar.gz': '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'},
-    {'HMMER-3.3.2_fix_perl.patch': '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d'},
-]
+checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
 
 builddependencies = [
-    ('Python', '3.10.8'),
-    ('Perl', '5.36.0'),
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
 ]
 
+# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files
+preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && "
+
 configopts = '--enable-mpi'
 
 buildopts = ' V=1 '

[smoors]

@ThomasHoffmann77 please keep the author info in the easyconfig?

[smoors]

@boegelbot: please test @ generoso

[boegelbot]

@smoors: Request for testing this PR well received on login1

PR test command 'EB_PR=22172 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22172 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14951

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/329412b97179d04e7fc642a0ac7f8c94 for a full test report.

[smoors]

@boegelbot please test @ jsc-zen3

[boegelbot]

@smoors: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=22172 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22172 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5547

Test results coming soon (I hope)...

Details

- notification for comment with ID 2598416498 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/a98fb6a7f98eecd1d6e9958a3a19984f for a full test report.

[smoors]

lgtm

[smoors]

Going in, thanks @ThomasHoffmann77!