add missing dependencies (TSEBRA, compleasm) + use more recent AUGUSTUS version for BRAKER v3.0.8 by boegel · Pull Request #21837 · easybuilders/easybuild-easyconfigs

boegel · 2024-11-12T16:38:20Z

(created using eb --new-pr)

To fix errors like:

 ERROR: in file /apps/gent/RHEL8/zen2-ib/software/BRAKER/3.0.8-foss-2023a/scripts/braker.pl at line 1832
$SRATOOLS_PATH not set!
There are 3 alternative ways to set SRATOOLS_PATH for
braker.pl:
   a) provide command-line argument --SRATOOLS_PATH=/your/path
   b) use an existing environment variable $SRATOOLS_PATH
      for setting the environment variable, run
           export SRATOOLS_PATH=/your/path
      in your shell. You may append this to your .bashrc or
      .profile file in order to make the variable available to
      all your bash sessions.
   c) braker.pl can try guessing the location of
      SRATOOLS_PATH from the location of fastq-dump
      executable if it is available in your $PATH variable.
      If you try to rely on this option, you can check by
      typing
           which fastq-dump
      in your shell, whether the executable is in your $PATH

jfgrimm · 2024-11-12T16:56:34Z

@boegelbot please test @ generoso

boegelbot · 2024-11-12T17:00:06Z

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

PR test command 'EB_PR=21837 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21837 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14694

Test results coming soon (I hope)...

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boegelbot · 2024-11-12T17:02:30Z

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/f40dba9f53cee418787c0b8618caf91d for a full test report.

…US dependency for BRAKER v3.0.8

github-actions · 2024-11-12T19:43:38Z

Updated software `AUGUSTUS-3.5.0-20240612-foss-2023a.eb`

Diff against AUGUSTUS-3.5.0-foss-2024a.eb

easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2024a.eb

diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2024a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
index 0dc95015db..f451e8926a 100644
--- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2024a.eb
+++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
@@ -5,43 +5,40 @@
 easyblock = 'ConfigureMake'
 
 name = 'AUGUSTUS'
-version = '3.5.0'
+version = '3.5.0-20240612'
+local_commit = '955ce17'
 
 homepage = 'https://bioinf.uni-greifswald.de/augustus/'
 description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 github_account = 'Gaius-Augustus'
 source_urls = [GITHUB_SOURCE]
-sources = ['v%(version)s.tar.gz']
-checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['f79a2b1b0dc7a773a499b39741810bf0af272b75d668af70004dd417cb161bec']
 
 builddependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.11.3'),
 ]
 
 dependencies = [
-    ('zlib', '1.3.1'),
-    ('Boost', '1.85.0'),
-    ('GSL', '2.8'),
-    ('SAMtools', '1.21'),
-    ('HTSlib', '1.21'),  # also provides tabix
-    ('BCFtools', '1.21'),
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
+    ('GSL', '2.7'),
+    ('SAMtools', '1.18'),
+    ('HTSlib', '1.18'),  # also provides tabix
+    ('BCFtools', '1.18'),
     ('lpsolve', '5.5.2.11'),
-    ('SuiteSparse', '7.10.1'),
+    ('SuiteSparse', '7.1.0'),
     ('BamTools', '2.5.2'),
-    ('SQLite', '3.45.3'),
+    ('SQLite', '3.42.0'),
 ]
 
 skipsteps = ['configure']
+
 # run "make clean" to avoid using binaries included with the source tarball
 prebuildopts = "make clean && "
-# fix_missing include <cstdint>
-prebuildopts += "sed -i 's/#include <sqlite3.h>/#include <sqlite3.h>\\n#include <cstdint>/g' "
-prebuildopts += "%(builddir)s/Augustus-%(version)s/include/sqliteDB.hh && "
-prebuildopts += "sed -i 's/#include <sqlite3.h>/#include <sqlite3.h>\\n#include <cstdint>/g' "
-prebuildopts += "%(builddir)s/Augustus-%(version)s/auxprogs/homGeneMapping/include/sqliteDB.hh && "
 
 _tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"'

Diff against AUGUSTUS-3.5.0-foss-2023a.eb

easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
index 2c31ade2eb..f451e8926a 100644
--- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
@@ -5,7 +5,8 @@
 easyblock = 'ConfigureMake'
 
 name = 'AUGUSTUS'
-version = '3.5.0'
+version = '3.5.0-20240612'
+local_commit = '955ce17'
 
 homepage = 'https://bioinf.uni-greifswald.de/augustus/'
 description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
@@ -14,8 +15,8 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 github_account = 'Gaius-Augustus'
 source_urls = [GITHUB_SOURCE]
-sources = ['v%(version)s.tar.gz']
-checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['f79a2b1b0dc7a773a499b39741810bf0af272b75d668af70004dd417cb161bec']
 
 builddependencies = [
     ('Python', '3.11.3'),

Diff against AUGUSTUS-3.5.0-foss-2022b.eb

easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
index b82557238d..f451e8926a 100644
--- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-20240612-foss-2023a.eb
@@ -1,36 +1,38 @@
 # Updated by: Pavel Grochal (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'ConfigureMake'
 
 name = 'AUGUSTUS'
-version = '3.5.0'
+version = '3.5.0-20240612'
+local_commit = '955ce17'
 
 homepage = 'https://bioinf.uni-greifswald.de/augustus/'
 description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 github_account = 'Gaius-Augustus'
 source_urls = [GITHUB_SOURCE]
-sources = ['v%(version)s.tar.gz']
-checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['f79a2b1b0dc7a773a499b39741810bf0af272b75d668af70004dd417cb161bec']
 
 builddependencies = [
-    ('Python', '3.10.8'),
+    ('Python', '3.11.3'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.12'),
-    ('Boost', '1.81.0'),
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
     ('GSL', '2.7'),
-    ('SAMtools', '1.17'),
-    ('HTSlib', '1.17'),  # also provides tabix
-    ('BCFtools', '1.17'),
+    ('SAMtools', '1.18'),
+    ('HTSlib', '1.18'),  # also provides tabix
+    ('BCFtools', '1.18'),
     ('lpsolve', '5.5.2.11'),
-    ('SuiteSparse', '5.13.0', '-METIS-5.1.0'),
+    ('SuiteSparse', '7.1.0'),
     ('BamTools', '2.5.2'),
-    ('SQLite', '3.39.4'),
+    ('SQLite', '3.42.0'),
 ]
 
 skipsteps = ['configure']

…asyconfigs into 20241112173815_new_pr_BRAKER308

boegel · 2025-04-08T11:22:41Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-04-08T11:30:10Z

@boegel: 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=21837 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21837 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6133

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 · 2025-04-08T11:35:41Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/d541ac6ba15111a943f681297ad662f3 for a full test report.

…asyconfigs into 20241112173815_new_pr_BRAKER308

PetrKralCZ · 2025-05-06T08:44:15Z

Add test exception for AUGUSTUS version required by BRAKER boegel/easybuild-easyconfigs#99

Add test exception for AUGUSTUS version required by BRAKER

boegel · 2025-05-20T08:32:01Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-20T08:40:08Z

@boegel: 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=21837 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21837 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6394

Test results coming soon (I hope)...

Details

- notification for comment with ID 2893455821 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 · 2025-05-20T08:45:30Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/1b397a762940f30b1a014fdd58d3e4e3 for a full test report.

laraPPr · 2025-05-23T13:45:14Z

Test report by @laraPPr
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4002.donphan.os - Linux RHEL 9.4 (Plow), x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), 1 x NVIDIA NVIDIA A2, 570.133.20, Python 3.11.3
See https://gist.github.com/laraPPr/bc5f12e812843819933d7be556bfa2ee for a full test report.

laraPPr

lgtm

laraPPr · 2025-05-23T13:50:48Z

Going in, thanks @boegel!

add missing SRA-Toolkit dependency for BRAKER v3.0.8

48271f8

github-actions Bot added the change label Nov 12, 2024

boegel added bug fix and removed change labels Nov 12, 2024

boegel added this to the release after 4.9.4 milestone Nov 12, 2024

boegel marked this pull request as draft November 12, 2024 16:52

boegel changed the title ~~add missing SRA-Toolkit dependency for BRAKER v3.0.8~~ add missing dependencies for BRAKER v3.0.8 Nov 12, 2024

add missing HISAT2, TSEBRA, compleasm dependency + use updated AUGUST…

51f6acf

…US dependency for BRAKER v3.0.8

github-actions Bot added change new update labels Nov 12, 2024

boegel changed the title ~~add missing dependencies for BRAKER v3.0.8~~ add missing dependencies (TSEBRA, compleasm) + use more recent AUGUSTUS version for BRAKER v3.0.8 Nov 13, 2024

boegel modified the milestones: release after 4.9.4, release after 5.0.0 Mar 18, 2025

PetrKralCZ mentioned this pull request Mar 28, 2025

Missing dependency TSEBRA for BRAKER vscentrum/vsc-software-stack#529

Closed

2 tasks

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

6d51a44

…asyconfigs into 20241112173815_new_pr_BRAKER308

PetrKralCZ and others added 2 commits May 6, 2025 09:39

test exception - AUGUSTUS version for BRAKER

430a89b

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

cb66461

…asyconfigs into 20241112173815_new_pr_BRAKER308

Merge pull request #99 from PetrKralCZ/tsebra_for_braker_tests

8d882c2

Add test exception for AUGUSTUS version required by BRAKER

laraPPr marked this pull request as ready for review May 13, 2025 11:06

boegel assigned laraPPr May 20, 2025

laraPPr approved these changes May 23, 2025

View reviewed changes

laraPPr merged commit 238d543 into easybuilders:develop May 23, 2025
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Updated software AUGUSTUS-3.5.0-20240612-foss-2023a.eb

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Updated software `AUGUSTUS-3.5.0-20240612-foss-2023a.eb`