{bio}[gompi/2023a] manta v1.6.0 w/ Python 2.7.18

[verdurin]

(created using eb --new-pr)

[github-actions]

Updated software manta-1.6.0-gompi-2023a-Python-2.7.18.eb

Diff against manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb

easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
index ff224b45ba..788ef2ad79 100644
--- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
@@ -1,6 +1,3 @@
-##
-# Authors::   Denis Kristak <[email protected]>
-##
 easyblock = 'CMakeMake'
 
 name = 'manta'
@@ -16,7 +13,7 @@ scores large-scale SVs, medium-sized indels and large insertions within a
 single efficient workflow.
 """
 
-toolchain = {'name': 'GCC', 'version': '10.2.0'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 
 github_account = 'Illumina'
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -24,42 +21,24 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421']
 
 builddependencies = [
-    ('CMake', '3.18.4'),
-    ('Doxygen', '1.8.20'),
+    ('CMake', '3.26.3'),
+    ('Doxygen', '1.9.7'),
 ]
 
 dependencies = [
     ('Python', '2.7.18'),
-    ('Boost', '1.74.0'),
-    ('zlib', '1.2.11'),
+    ('Boost', '1.75.0'),
+    ('zlib', '1.2.13'),
 ]
 
-# workaround for bug in Boost 1.74.0 triggered by use of -Wundef,
-# see https://github.com/easybuilders/easybuild-easyconfigs/issues/13337
-# and https://github.com/boostorg/type_traits/issues/107
-configopts = "-DBoost_NO_BOOST_CMAKE=ON"
-
-buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' "
-
-# following are necessary should anyone try to make manta compatible with python3
-# making included pyflow compatible with python3
-# preinstallopts = "sed -i 's/0755/0o755/g' ./redist/pyflow-*/src/pyflow.py && "
-# preinstallopts += "sed -i 's/DataDirException, e/DataDirException(e)/g' ./redist/pyflow-*/src/pyflow.py && "
-# preinstallopts += "sed -i 's/raise Exception(\"pyflow module has only been tested for python versions \
-# \[2.4,3.0)/pass #/g' ./redist/pyflow-*/src/pyflow.py && "
-# preinstallopts += "sed -i 's/raise Exception(\"Manta does not currently support python3/pass #/g' \
-# ../manta-%(version)s/src/python/lib/makeRunScript.py && "
-
 local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats',
                   'GetChromDepth', 'MergeAlignmentStats', 'MergeSVLoci', 'SummarizeAlignmentStats', 'SummarizeSVLoci',
                   'TestAssembler']
 
 sanity_check_paths = {
-    'files': [
-        ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] +
-        ['libexec/%s' % x for x in ['denovo_scoring.py', 'extractSmallIndelCandidates.py']],
-    ],
-    'dirs': ['libexec'],
+    'files': ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] +
+             ['libexec/%s' % x for x in local_binaries],
+    'dirs': ['lib/python', 'share'],
 }
 
 sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py']

Diff against manta-1.6.0-gompi-2020a-Python-2.7.18.eb

easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
index 7633e9131e..788ef2ad79 100644
--- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
@@ -13,7 +13,7 @@ scores large-scale SVs, medium-sized indels and large insertions within a
 single efficient workflow.
 """
 
-toolchain = {'name': 'gompi', 'version': '2020a'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 
 github_account = 'Illumina'
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -21,14 +21,14 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421']
 
 builddependencies = [
-    ('CMake', '3.16.4'),
-    ('Doxygen', '1.8.17'),
+    ('CMake', '3.26.3'),
+    ('Doxygen', '1.9.7'),
 ]
 
 dependencies = [
     ('Python', '2.7.18'),
-    ('Boost', '1.72.0'),
-    ('zlib', '1.2.11'),
+    ('Boost', '1.75.0'),
+    ('zlib', '1.2.13'),
 ]
 
 local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats',

Diff against manta-1.6.0-gompi-2019b-Python-2.7.16.eb

easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb

diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
index 2d6c80a9b7..788ef2ad79 100644
--- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb
+++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2023a-Python-2.7.18.eb
@@ -13,7 +13,7 @@ scores large-scale SVs, medium-sized indels and large insertions within a
 single efficient workflow.
 """
 
-toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 
 github_account = 'Illumina'
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -21,14 +21,14 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421']
 
 builddependencies = [
-    ('CMake', '3.15.3'),
-    ('Doxygen', '1.8.16'),
+    ('CMake', '3.26.3'),
+    ('Doxygen', '1.9.7'),
 ]
 
 dependencies = [
-    ('Python', '2.7.16'),
-    ('Boost', '1.71.0'),
-    ('zlib', '1.2.11'),
+    ('Python', '2.7.18'),
+    ('Boost', '1.75.0'),
+    ('zlib', '1.2.13'),
 ]
 
 local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats',

[verdurin]

@boegelbot please test @ jsc-zen3

[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/45486c107d9b3e53499784a070266e48 for a full test report.

[boegelbot]

@verdurin: 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=22040 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22040 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5452

Test results coming soon (I hope)...

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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]

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/17e68930d2624733edef7f541343c8ac for a full test report.