{bio}[foss/2023b] BEDOPS v2.4.41

[PetrKralCZ]

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#438

[github-actions]

Updated software BEDOPS-2.4.41-foss-2023b.eb

Diff against BEDOPS-2.4.41-foss-2021b.eb

easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb

diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
index 2a76d9d7b5..d6a87743c8 100644
--- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb
+++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
@@ -1,5 +1,6 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
 
 easyblock = 'MakeCp'
 
@@ -12,7 +13,7 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig
  other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for
  distributing whole-genome analyses across a computational cluster."""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']

Diff against BEDOPS-2.4.35-foss-2018b.eb

easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.35-foss-2018b.eb

diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.35-foss-2018b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
index 6d37ee720d..d6a87743c8 100644
--- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.35-foss-2018b.eb
+++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
@@ -1,9 +1,11 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
 
 easyblock = 'MakeCp'
 
 name = 'BEDOPS'
-version = '2.4.35'
+version = '2.4.41'
 
 homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html'
 description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and
@@ -11,14 +13,14 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig
  other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for
  distributing whole-genome analyses across a computational cluster."""
 
-toolchain = {'name': 'foss', 'version': '2018b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['da0265cf55ef5094834318f1ea4763d7a3ce52a6900e74f532dd7d3088c191fa']
+checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194']
 
-# else build of jansson library fails with: "configure: error: C compiler cannot create executables"
+# else build of jansson library fails with: 'configure: error: C compiler cannot create executables'
 prebuildopts = 'unset LIBS && '
 # builds all variants and copies executables to bin directory
 buildopts = ' all && make install'
@@ -28,7 +30,9 @@ keepsymlinks = True
 files_to_copy = ['bin']
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch']],
+    'files': [
+        'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch']
+    ],
     'dirs': [],
 }
 

Diff against BEDOPS-2.4.32-intel-2018a.eb

easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.32-intel-2018a.eb

diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.32-intel-2018a.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
index 9ee0318302..d6a87743c8 100644
--- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.32-intel-2018a.eb
+++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb
@@ -1,9 +1,11 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
 
 easyblock = 'MakeCp'
 
 name = 'BEDOPS'
-version = '2.4.32'
+version = '2.4.41'
 
 homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html'
 description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and
@@ -11,24 +13,26 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig
  other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for
  distributing whole-genome analyses across a computational cluster."""
 
-toolchain = {'name': 'intel', 'version': '2018a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['2039c55d66ac68e5083b7dbcb5b83d232db0877aa60f2bf766d90a14438c8178']
+checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194']
 
-# else build of jansson library fails with: "configure: error: C compiler cannot create executables"
+# else build of jansson library fails with: 'configure: error: C compiler cannot create executables'
 prebuildopts = 'unset LIBS && '
 # builds all variants and copies executables to bin directory
-buildopts = ' all CC="$CC" CXX="$CXX" && make install'
+buildopts = ' all && make install'
 # actually used variant is linked to via symlinks
 keepsymlinks = True
 
 files_to_copy = ['bin']
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch']],
+    'files': [
+        'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch']
+    ],
     'dirs': [],
 }
 

[PetrKralCZ]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=21810 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21810 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14666

Test results coming soon (I hope)...

- notification for comment with ID 2464654103 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)
cns2 - 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/dd6ce8ef045c9333806e1ea8fafdbbd3 for a full test report.

[PetrKralCZ]

@boegelbot please test @ jsc-zen3

[boegelbot]

@PetrKralCZ: 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=21810 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21810 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5231

Test results coming soon (I hope)...

- notification for comment with ID 2464688829 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 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/f65343c0e2b66d942be29a79200a6945 for a full test report.