Skip to content

{bio}[gompi/2024a] HMMER v3.4#22172

Merged
smoors merged 2 commits intoeasybuilders:developfrom
ThomasHoffmann77:20250116173609_new_pr_HMMER34
Jan 17, 2025
Merged

{bio}[gompi/2024a] HMMER v3.4#22172
smoors merged 2 commits intoeasybuilders:developfrom
ThomasHoffmann77:20250116173609_new_pr_HMMER34

Conversation

@ThomasHoffmann77
Copy link
Contributor

@ThomasHoffmann77 ThomasHoffmann77 commented Jan 16, 2025

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

@github-actions
Copy link

github-actions bot commented Jan 16, 2025

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
Copy link
Contributor

smoors commented Jan 17, 2025

@ThomasHoffmann77 please keep the author info in the easyconfig?

@jpecar Can you please check the header I added?
@smoors
Copy link
Contributor

smoors commented Jan 17, 2025

@boegelbot: please test @ generoso

@boegelbot
Copy link
Collaborator

@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

- notification for comment with ID 2598318566 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
Copy link
Collaborator

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
Copy link
Contributor

smoors commented Jan 17, 2025

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

@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
Copy link
Collaborator

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 smoors added this to the release after 4.9.4 milestone Jan 17, 2025
Copy link
Contributor

@smoors smoors left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@smoors
Copy link
Contributor

smoors commented Jan 17, 2025

Going in, thanks @ThomasHoffmann77!

@smoors smoors merged commit 32ca98b into easybuilders:develop Jan 17, 2025
10 checks passed
@boegel boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

Projects

None yet

Development

Successfully merging this pull request may close these issues.

4 participants