{bio}[foss/2023a] HOMER v5.1 w/ R 4.3.2

[verdurin]

(created using eb --new-pr)

[github-actions]

Updated software HOMER-5.1-foss-2023a-R-4.3.2.eb

Diff against HOMER-4.11.1-foss-2022b.eb

easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb
index 0131cad977..554852bed5 100644
--- a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb
@@ -1,47 +1,38 @@
 easyblock = 'Binary'
 
 name = 'HOMER'
-version = '4.11.1'
+version = '5.1'
+versionsuffix = '-R-%(rver)s'
 
-homepage = 'http://homer.ucsd.edu/homer/'
+homepage = "http://homer.ucsd.edu/homer/"
 description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and
-next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written
-in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding
-8-20 bp motifs in large scale genomics data.  HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq,
-RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets."""
+ next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written
+ in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding
+ 8-20 bp motifs in large scale genomics data.  HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq,
+ RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
-source_urls = ['http://homer.ucsd.edu/homer/data/software']
-sources = ['homer.v%(version)s.zip']
-checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
-
-extract_sources = True
+source_urls = ['http://homer.ucsd.edu/homer']
+sources = ['configureHomer.pl']
+checksums = ['ccdaa3004a0e0df0882634671d4a1acc88364761e0e6c7ea329ebbf1eb729537']
 
 builddependencies = [
-    ('wget', '1.21.4'),
+    ('wget', '1.24.5'),
     ('Zip', '3.0'),
     ('UnZip', '6.0'),
 ]
 
 dependencies = [
-    ('Perl', '5.36.0'),
-    ('weblogo', '2.8.2'),
-    ('SAMtools', '1.17'),
-    ('Kent_tools', '461'),
-    ('R', '4.2.2'),
-    ('R-bundle-Bioconductor', '3.16', '-R-4.2.2')
+    ('Perl', '5.36.1'),
+    ('R', '4.3.2'),
+    ('SAMtools', '1.18'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix)
 ]
 
-buildininstalldir = True
-skipsteps = ['install']
-
-# This installs the entire suite, to install only base Homer package run :
-# cd %(installdir)s; perl ./configureHomer.pl -install homer
-postinstallcmds = ['perl ./configureHomer.pl -install -all -keepScript']
+postinstallcmds = ["cd %(installdir)s && perl ./configureHomer.pl -install homer -version v%(version)s"]
 
 sanity_check_paths = {
-    'dirs': ['bin', 'data', 'motifs', 'update'],
     'files': [
         'bin/homer',
         'bin/getGenomeTilingPeaks',
@@ -50,6 +41,7 @@ sanity_check_paths = {
         'data/accession/homologene.data',
         'motifs/hnf1b.motif',
     ],
+    'dirs': ['bin', 'data', 'motifs', 'update'],
 }
 
 sanity_check_commands = ["%(namelower)s --help"]

Diff against HOMER-4.11-foss-2023a-R-4.3.2.eb

easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb
index 49de16a3d9..554852bed5 100644
--- a/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb
@@ -1,7 +1,7 @@
 easyblock = 'Binary'
 
 name = 'HOMER'
-version = '4.11'
+version = '5.1'
 versionsuffix = '-R-%(rver)s'
 
 homepage = "http://homer.ucsd.edu/homer/"

[verdurin]

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/ac2beda4663b914d1ac6c21e30cf0476 for a full test report.

[boegel]

lgtm

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3105.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/0c28c70b18186eee58a6de7c51b0a334 for a full test report.

[boegel]

@boegelbot please test @ jsc-zen3

[boegelbot]

@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=21829 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21829 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5412

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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[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 3.9.19
See https://gist.github.com/boegelbot/9bb0aaeec3a34c8d6a264708469a336f for a full test report.

[boegel]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=21829 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21829 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14835

Test results coming soon (I hope)...

- notification for comment with ID 2525549499 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)
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/b5c167bf5b4cf7fe5120467d878826d0 for a full test report.

[boegel]

Going in, thanks @verdurin!