add patch for HMMER v3.4 to add support for `--seq_limit` option by ThomasHoffmann77 · Pull Request #24301 · easybuilders/easybuild-easyconfigs

ThomasHoffmann77 · 2025-10-20T07:48:12Z

(created using eb --new-pr)

…MER-3.4.0_AF3_jackhmmer_seq_limit.patch

github-actions · 2025-10-20T07:48:43Z

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

Diff against HMMER-3.4-gompi-2024a.eb

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a-seqlimit.eb
index 5e40c90494..e3005576ce 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a-seqlimit.eb
@@ -6,6 +6,7 @@
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
 #             Jure Pečar (EMBL)
+#             Thomas Hoffmann (EMBL): seq_limit
 # License::   MIT/GPL
 # $Id$
 #
@@ -18,6 +19,7 @@ easyblock = 'ConfigureMake'
 
 name = 'HMMER'
 version = '3.4'
+versionsuffix = '-seqlimit'
 
 homepage = 'http://hmmer.org/'
 description = """HMMER is used for searching sequence databases for homologs
@@ -28,7 +30,8 @@ description = """HMMER is used for searching sequence databases for homologs
  HMMER aims to be significantly more accurate and more able to detect remote
  homologs because of the strength of its underlying mathematical models. In the
  past, this strength came at significant computational expense, but in the new
- HMMER3 project, HMMER is now essentially as fast as BLAST."""
+ HMMER3 project, HMMER is now essentially as fast as BLAST.
+Patched according to https://github.com/google-deepmind/alphafold3/issues/525"""
 
 toolchain = {'name': 'gompi', 'version': '2024a'}
 
@@ -37,7 +40,11 @@ source_urls = [
     'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
+patches = ['HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch']
+checksums = [
+    {'hmmer-3.4.tar.gz': 'ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'},
+    {'HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch': 'd994d6eae98c7247b3fc777d7d704d48fef037eccb6d55a50d8a603d6b1b29e2'},
+]
 
 builddependencies = [
     ('Python', '3.12.3'),
@@ -74,6 +81,7 @@ sanity_check_commands = [
     "esl-construct -h",
     "hmmsearch -h",
     "nhmmer -h",
+    "jackhmmer -h grep seq_limit",
 ]
 
 moduleclass = 'bio'

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-seqlimit.eb
index bb76dc1e93..e3005576ce 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a-seqlimit.eb
@@ -5,6 +5,8 @@
 # Authors::   Nils Christian <nils.christian@uni.lu>,
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
+#             Thomas Hoffmann (EMBL): seq_limit
 # License::   MIT/GPL
 # $Id$
 #
@@ -17,6 +19,7 @@ easyblock = 'ConfigureMake'
 
 name = 'HMMER'
 version = '3.4'
+versionsuffix = '-seqlimit'
 
 homepage = 'http://hmmer.org/'
 description = """HMMER is used for searching sequence databases for homologs
@@ -27,20 +30,25 @@ description = """HMMER is used for searching sequence databases for homologs
  HMMER aims to be significantly more accurate and more able to detect remote
  homologs because of the strength of its underlying mathematical models. In the
  past, this strength came at significant computational expense, but in the new
- HMMER3 project, HMMER is now essentially as fast as BLAST."""
+ HMMER3 project, HMMER is now essentially as fast as BLAST.
+Patched according to https://github.com/google-deepmind/alphafold3/issues/525"""
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+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]
-checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
+patches = ['HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch']
+checksums = [
+    {'hmmer-3.4.tar.gz': 'ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'},
+    {'HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch': 'd994d6eae98c7247b3fc777d7d704d48fef037eccb6d55a50d8a603d6b1b29e2'},
+]
 
 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
@@ -73,6 +81,7 @@ sanity_check_commands = [
     "esl-construct -h",
     "hmmsearch -h",
     "nhmmer -h",
+    "jackhmmer -h grep seq_limit",
 ]
 
 moduleclass = 'bio'

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-seqlimit.eb
index 99f585d998..e3005576ce 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a-seqlimit.eb
@@ -5,6 +5,8 @@
 # Authors::   Nils Christian <nils.christian@uni.lu>,
 #             Fotis Georgatos <fotis@cern.ch>
 # Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
+#             Thomas Hoffmann (EMBL): seq_limit
 # License::   MIT/GPL
 # $Id$
 #
@@ -17,6 +19,7 @@ easyblock = 'ConfigureMake'
 
 name = 'HMMER'
 version = '3.4'
+versionsuffix = '-seqlimit'
 
 homepage = 'http://hmmer.org/'
 description = """HMMER is used for searching sequence databases for homologs
@@ -27,20 +30,25 @@ description = """HMMER is used for searching sequence databases for homologs
  HMMER aims to be significantly more accurate and more able to detect remote
  homologs because of the strength of its underlying mathematical models. In the
  past, this strength came at significant computational expense, but in the new
- HMMER3 project, HMMER is now essentially as fast as BLAST."""
+ HMMER3 project, HMMER is now essentially as fast as BLAST.
+Patched according to https://github.com/google-deepmind/alphafold3/issues/525"""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+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]
-checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
+patches = ['HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch']
+checksums = [
+    {'hmmer-3.4.tar.gz': 'ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'},
+    {'HMMER-3.4.0_AF3_jackhmmer_seq_limit.patch': 'd994d6eae98c7247b3fc777d7d704d48fef037eccb6d55a50d8a603d6b1b29e2'},
+]
 
 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
@@ -73,6 +81,7 @@ sanity_check_commands = [
     "esl-construct -h",
     "hmmsearch -h",
     "nhmmer -h",
+    "jackhmmer -h grep seq_limit",
 ]
 
 moduleclass = 'bio'

pavelToman · 2025-10-20T09:38:48Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4301.litleo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9454P 48-Core Processor, 1 x NVIDIA NVIDIA H100 NVL, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/c45c390b0418e7e08d65bef88ffeb1c5 for a full test report.

Crivella · 2025-10-20T10:48:38Z

If i understand correctly this is adding a CLI option to jackhammer.
If that is the case i think it would make sense to change the original EC instead of creating a suffixed version (especially if this patch is gonna be upstream in future releases)

pavelToman · 2025-10-20T12:02:55Z

@boegelbot please test @ jsc-zen3-a100

boegelbot · 2025-10-20T12:10:09Z

@pavelToman: 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=24301 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24301 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8492

Test results coming soon (I hope)...

Details

- notification for comment with ID 3421781828 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 · 2025-10-20T12:14:44Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 580.95.05, Python 3.9.21
See https://gist.github.com/boegelbot/16e3ec0ab225d3d591b1b25d502c21ff for a full test report.

boegel

@ThomasHoffmann77 Since the patch is only adding an option, I would apply it in the existing easyconfig HMMER-3.4-gompi-2024a.eb, rather than introducing a new variant...

…i-2024a.eb remove versionsuffix

ThomasHoffmann77 · 2025-11-21T08:57:56Z

@ThomasHoffmann77 Since the patch is only adding an option, I would apply it in the existing easyconfig HMMER-3.4-gompi-2024a.eb, rather than introducing a new variant...

I removed the versionsuffix and renamed the file

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb

Crivella · 2025-11-26T10:10:07Z

Test report by @Crivella
SUCCESS
Build succeeded for 1 out of 1 (total: 4 mins 0 secs) (1 easyconfigs in total)
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.14
See https://gist.github.com/Crivella/53871503ad379c49e38f43b300bef8bb for a full test report.

Crivella · 2025-11-26T10:11:18Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-11-26T10:20:13Z

@Crivella: 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=24301 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24301 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8912

Test results coming soon (I hope)...

Details

- notification for comment with ID 3580585166 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 · 2025-11-26T10:24:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 4 mins 23 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/bcf5b1df12f836cf0cfde54254fcae0c for a full test report.

Crivella

LGTM

Required changes applied

Crivella · 2025-11-26T10:27:10Z

Going in, thanks @ThomasHoffmann77!

adding easyconfigs: HMMER-3.4-gompi-2024a-seqlimit.eb and patches: HM…

886da6f

…MER-3.4.0_AF3_jackhmmer_seq_limit.patch

github-actions bot added the update label Oct 20, 2025

ThomasHoffmann77 mentioned this pull request Oct 20, 2025

{ai}[foss/2024a] AlphaFold3 v3.0.1-20250908, dm-haiku v0.0.14, Flax v0.10.2, ... w/ CUDA 12.6.0 #24177

Open

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Oct 20, 2025

Thyre added this to the next release (5.2.0?) milestone Oct 20, 2025

boegel previously requested changes Oct 21, 2025

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ThomasHoffmann77 added 2 commits November 21, 2025 09:54

Delete easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb

1f35f33

Update and rename HMMER-3.4-gompi-2024a-seqlimit.eb to HMMER-3.4-gomp…

c0578c1

…i-2024a.eb remove versionsuffix

github-actions bot added change and removed update labels Nov 21, 2025

Crivella requested changes Nov 26, 2025

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easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb Outdated Show resolved Hide resolved

Update easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb

2ce8d43

Crivella added enhancement and removed change labels Nov 26, 2025

Crivella approved these changes Nov 26, 2025

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Crivella merged commit 7ea8039 into easybuilders:develop Nov 26, 2025
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boegel changed the title ~~{bio}[gompi/2024a] HMMER v3.4 w/ seqlimit~~ add patch for HMMER v3.4 to add support for --seq_limit option Dec 23, 2025

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

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ThomasHoffmann77 commented Oct 20, 2025 •

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