{bio,data}[GCC/12.3.0] Minimac4 v4.1.6, savvy v2.1.0, shrinkwrap v1.2.0, ... by verdurin · Pull Request #22307 · easybuilders/easybuild-easyconfigs

verdurin · 2025-02-13T15:16:42Z

(created using eb --new-pr)

…3.0.eb, shrinkwrap-1.2.0-GCCcore-12.3.0.eb, omp-1.0.0-GCC-12.3.0.eb, libStatGen-1.0.15-GCCcore-12.3.0.eb

github-actions · 2025-02-13T15:17:13Z

Updated software `libStatGen-1.0.15-GCCcore-12.3.0.eb`

Diff against libStatGen-1.0.15-GCCcore-10.2.0.eb

easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-12.3.0.eb
index 6cb6951226..025a71f407 100644
--- a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-12.3.0.eb
@@ -3,31 +3,32 @@ easyblock = 'MakeCp'
 
 name = 'libStatGen'
 version = '1.0.15'
-_hash = 'ff4f2fc'
 
-homepage = "https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen"
-description = """Useful set of classes for creating statistical genetic programs."""
+homepage = 'https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen'
+description = "Useful set of classes for creating statistical genetic programs."
 
-toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-github_account = 'statgen'
 source_urls = [GITHUB_SOURCE]
-sources = [{'download_filename': '%s.tar.gz' % _hash, 'filename': SOURCELOWER_TAR_GZ}]
+sources = [{'download_filename': 'ff4f2fc.tar.gz', 'filename': SOURCELOWER_TAR_GZ}]
 checksums = ['68acb15b6c85f07b0dbf3f8b7a2a99a88fc97d3e29e80bebab82bd2a8e09121e']
 
-builddependencies = [('binutils', '2.35')]
-
-dependencies = [('zlib', '1.2.11')]
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+]
 
+github_account = 'statgen'
 runtest = 'test'
-
 files_to_copy = [
-    (['libStatGen.a'], 'lib'),
-    ('include'),
+    (['%(name)s.a'], 'lib'),
+    'include',
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libStatGen.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'],
+    'files': ['lib/%(name)s.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'],
     'dirs': [],
 }

Diff against libStatGen-20190330-GCCcore-6.4.0.eb

easybuild/easyconfigs/l/libStatGen/libStatGen-20190330-GCCcore-6.4.0.eb

diff --git a/easybuild/easyconfigs/l/libStatGen/libStatGen-20190330-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-12.3.0.eb
index 87c89071a0..025a71f407 100644
--- a/easybuild/easyconfigs/l/libStatGen/libStatGen-20190330-GCCcore-6.4.0.eb
+++ b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-12.3.0.eb
@@ -2,32 +2,33 @@
 easyblock = 'MakeCp'
 
 name = 'libStatGen'
-version = '20190330'
-_hash = '457bf9e'
+version = '1.0.15'
 
-homepage = "https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen"
-description = """Useful set of classes for creating statistical genetic programs."""
+homepage = 'https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen'
+description = "Useful set of classes for creating statistical genetic programs."
 
-toolchain = {'name': 'GCCcore', 'version': '6.4.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-github_account = 'statgen'
 source_urls = [GITHUB_SOURCE]
-sources = [{'download_filename': '%s.tar.gz' % _hash, 'filename': SOURCELOWER_TAR_GZ}]
-checksums = ['3ecaab2f76e54a40977beb33695e90d89c2473a010617fecd1e4aa0fa9ee824d']
-
-builddependencies = [('binutils', '2.28')]
+sources = [{'download_filename': 'ff4f2fc.tar.gz', 'filename': SOURCELOWER_TAR_GZ}]
+checksums = ['68acb15b6c85f07b0dbf3f8b7a2a99a88fc97d3e29e80bebab82bd2a8e09121e']
 
-dependencies = [('zlib', '1.2.11')]
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+]
 
+github_account = 'statgen'
 runtest = 'test'
-
 files_to_copy = [
-    (['libStatGen.a'], 'lib'),
-    ('include'),
+    (['%(name)s.a'], 'lib'),
+    'include',
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libStatGen.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'],
+    'files': ['lib/%(name)s.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'],
     'dirs': [],
 }

Updated software `Minimac4-4.1.6-GCC-12.3.0.eb`

Diff against Minimac4-1.0.0-foss-2018a.eb

easybuild/easyconfigs/m/Minimac4/Minimac4-1.0.0-foss-2018a.eb

diff --git a/easybuild/easyconfigs/m/Minimac4/Minimac4-1.0.0-foss-2018a.eb b/easybuild/easyconfigs/m/Minimac4/Minimac4-4.1.6-GCC-12.3.0.eb
index 9dc99a0a7a..b8754abc1c 100644
--- a/easybuild/easyconfigs/m/Minimac4/Minimac4-1.0.0-foss-2018a.eb
+++ b/easybuild/easyconfigs/m/Minimac4/Minimac4-4.1.6-GCC-12.3.0.eb
@@ -3,7 +3,7 @@
 easyblock = 'CMakeMake'
 
 name = 'Minimac4'
-version = '1.0.0'
+version = '4.1.6'
 
 homepage = 'https://genome.sph.umich.edu/wiki/Minimac4'
 description = """Minimac4 is a latest version in the series of genotype imputation software
@@ -11,17 +11,21 @@ description = """Minimac4 is a latest version in the series of genotype imputati
  Minimac4 is a lower memory and more computationally efficient implementation
  of the original algorithms with comparable imputation quality."""
 
-toolchain = {'name': 'foss', 'version': '2018a'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/statgen/%(name)s/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['c15e276c7ee36d6c553d59f8ff98c0f906e7d53a34ed2b25570098040e2631a7']
+checksums = ['0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333']
 
-builddependencies = [('CMake', '3.10.2')]
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
 
 dependencies = [
-    ('zlib', '1.2.11'),
-    ('libStatGen', '20190330'),
+    ('zlib', '1.2.13'),
+    ('libStatGen', '1.0.15'),
+    ('savvy', '2.1.0'),
+    ('omp', '1.0.0'),
 ]
 
 sanity_check_paths = {

Updated software `savvy-2.1.0-GCC-12.3.0.eb`

Diff against savvy-1.3.0-GCC-8.2.0-2.31.1.eb

easybuild/easyconfigs/s/savvy/savvy-1.3.0-GCC-8.2.0-2.31.1.eb

diff --git a/easybuild/easyconfigs/s/savvy/savvy-1.3.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/savvy/savvy-2.1.0-GCC-12.3.0.eb
index 084b6e0e5b..e148f2ea5b 100644
--- a/easybuild/easyconfigs/s/savvy/savvy-1.3.0-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/s/savvy/savvy-2.1.0-GCC-12.3.0.eb
@@ -1,35 +1,34 @@
 # This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+
 easyblock = 'CMakeMake'
 
 name = 'savvy'
-version = '1.3.0'
+version = '2.1.0'
 
-homepage = "https://github.com/statgen/savvy"
-description = """Interface to various variant calling formats."""
+homepage = 'https://github.com/statgen/savvy'
+description = "Interface to various variant calling formats."
 
-toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://github.com/statgen/savvy/archive']
+source_urls = ['https://github.com/statgen/%(name)s/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['5fbf25ff0793de769f12d2a9e0a0f0f40dc3d315cbdbcd16fc6ab90949bfa172']
+checksums = ['83ebd88c097799b3bbf771dc8ebf6892797ca7a1f49c2d1665d52cfc1bf9e1de']
 
 builddependencies = [
-    ('binutils', '2.31.1'),
-    ('CMake', '3.13.3'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
 ]
 
 dependencies = [
-    ('bzip2', '1.0.6'),
-    ('cURL', '7.63.0'),
-    ('HTSlib', '1.9'),
-    ('shrinkwrap', '1.0.0-beta'),
-    ('XZ', '5.2.4'),
-    ('zstd', '1.4.0'),
+    ('bzip2', '1.0.8'),
+    ('cURL', '8.0.1'),
+    ('HTSlib', '1.18'),
+    ('shrinkwrap', '1.2.0'),
+    ('XZ', '5.4.2'),
+    ('zstd', '1.5.5'),
 ]
 
-preconfigopts = "export LDFLAGS='-lcurl -lhts' && "
-
 sanity_check_paths = {
     'files': ['bin/sav'],
     'dirs': [],

Updated software `shrinkwrap-1.2.0-GCCcore-12.3.0.eb`

Diff against shrinkwrap-1.1.0-GCCcore-10.2.0.eb

easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.2.0-GCCcore-12.3.0.eb
index a9387c69f6..96020a6007 100644
--- a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.2.0-GCCcore-12.3.0.eb
@@ -2,29 +2,29 @@
 easyblock = 'CMakeMake'
 
 name = 'shrinkwrap'
-version = '1.1.0'
+version = '1.2.0'
 
-homepage = "https://github.com/jonathonl/shrinkwrap"
-description = """A std::streambuf wrapper for compression formats."""
+homepage = 'https://github.com/jonathonl/shrinkwrap'
+description = "A std::streambuf wrapper for compression formats."
 
-toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-source_urls = ['https://github.com/jonathonl/shrinkwrap/archive']
+source_urls = ['https://github.com/jonathonl/%(name)s/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['833e85bdc41e7bf82a57f0fb52958795fb089f691981d2e3a2b68eee17128082']
+checksums = ['aa15583079c3dfccb118cf36fae9bc6353920b99d0204a9e349dad027b531286']
 
 builddependencies = [
-    ('binutils', '2.35'),
-    ('CMake', '3.18.4'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
 ]
 
 dependencies = [
-    ('XZ', '5.2.5'),
-    ('zstd', '1.4.5'),
+    ('XZ', '5.4.2'),
+    ('zstd', '1.5.5'),
 ]
 
 sanity_check_paths = {
-    'files': ['include/%%(name)s/%s.hpp' % i for i in ['gz', 'istream', 'xz', 'zstd']],
+    'files': ['include/shrinkwrap/%s' % x for x in ['istream.hpp', 'stdio.hpp', 'zstd.hpp']],
     'dirs': [],
 }

Diff against shrinkwrap-1.0.0-beta-GCCcore-8.2.0.eb

easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.0.0-beta-GCCcore-8.2.0.eb

diff --git a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.0.0-beta-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.2.0-GCCcore-12.3.0.eb
index cb3b063189..96020a6007 100644
--- a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.0.0-beta-GCCcore-8.2.0.eb
+++ b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.2.0-GCCcore-12.3.0.eb
@@ -2,29 +2,29 @@
 easyblock = 'CMakeMake'
 
 name = 'shrinkwrap'
-version = '1.0.0-beta'
+version = '1.2.0'
 
-homepage = "https://github.com/jonathonl/shrinkwrap"
-description = """A std::streambuf wrapper for compression formats."""
+homepage = 'https://github.com/jonathonl/shrinkwrap'
+description = "A std::streambuf wrapper for compression formats."
 
-toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-source_urls = ['https://github.com/jonathonl/shrinkwrap/archive']
+source_urls = ['https://github.com/jonathonl/%(name)s/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['c9e7e7eb4ea7ea85ddffd0d7ecdc2febdcac8486d178cdc99d762404fe3bb8dd']
+checksums = ['aa15583079c3dfccb118cf36fae9bc6353920b99d0204a9e349dad027b531286']
 
 builddependencies = [
-    ('binutils', '2.31.1'),
-    ('CMake', '3.13.3'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
 ]
 
 dependencies = [
-    ('XZ', '5.2.4'),
-    ('zstd', '1.4.0'),
+    ('XZ', '5.4.2'),
+    ('zstd', '1.5.5'),
 ]
 
 sanity_check_paths = {
-    'files': ['include/%%(name)s/%s.hpp' % i for i in ['gz', 'istream', 'xz', 'zstd']],
+    'files': ['include/shrinkwrap/%s' % x for x in ['istream.hpp', 'stdio.hpp', 'zstd.hpp']],
     'dirs': [],
 }

verdurin · 2025-02-13T15:32:24Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-02-13T15:40:09Z

@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=22307 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22307 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5711

Test results coming soon (I hope)...

Details

- notification for comment with ID 2656972203 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 · 2025-02-13T15:45:22Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 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/40806ee716e9a999b273044fba7094b0 for a full test report.

verdurin · 2025-02-13T15:49:56Z

Test report by @verdurin
SUCCESS
Build succeeded for 5 out of 5 (5 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/12eadc78150e3f72634141a873e212a9 for a full test report.

branfosj · 2025-02-15T13:27:46Z

Test report by @branfosj
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/116adac046d463eec422d64183c51638 for a full test report.

branfosj · 2025-02-15T13:28:58Z

Going in, thanks @verdurin!

adding easyconfigs: Minimac4-4.1.6-GCC-12.3.0.eb, savvy-2.1.0-GCC-12.…

b80348a

…3.0.eb, shrinkwrap-1.2.0-GCCcore-12.3.0.eb, omp-1.0.0-GCC-12.3.0.eb, libStatGen-1.0.15-GCCcore-12.3.0.eb

verdurin added new update labels Feb 13, 2025

remove f-string

9031c33

software added 2 commits February 13, 2025 16:04

Add checksum and fix layout

16012a8

Fix long line

bc0d8d5

branfosj added this to the release after 4.9.4 milestone Feb 15, 2025

branfosj approved these changes Feb 15, 2025

View reviewed changes

branfosj merged commit e80e8eb into easybuilders:develop Feb 15, 2025

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

{bio,data}[GCC/12.3.0] Minimac4 v4.1.6, savvy v2.1.0, shrinkwrap v1.2.0, ...#22307

{bio,data}[GCC/12.3.0] Minimac4 v4.1.6, savvy v2.1.0, shrinkwrap v1.2.0, ...#22307
branfosj merged 4 commits intoeasybuilders:developfrom
verdurin:20250213151637_new_pr_Minimac4416

verdurin commented Feb 13, 2025

Uh oh!

github-actions Bot commented Feb 13, 2025 •

edited

Loading

Uh oh!

verdurin commented Feb 13, 2025

Uh oh!

boegelbot commented Feb 13, 2025

Uh oh!

boegelbot commented Feb 13, 2025

Uh oh!

verdurin commented Feb 13, 2025

Uh oh!

branfosj commented Feb 15, 2025

Uh oh!

branfosj commented Feb 15, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

verdurin commented Feb 13, 2025

Uh oh!

github-actions Bot commented Feb 13, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Updated software libStatGen-1.0.15-GCCcore-12.3.0.eb

Updated software Minimac4-4.1.6-GCC-12.3.0.eb

Updated software savvy-2.1.0-GCC-12.3.0.eb

Updated software shrinkwrap-1.2.0-GCCcore-12.3.0.eb

Uh oh!

verdurin commented Feb 13, 2025

Uh oh!

boegelbot commented Feb 13, 2025

Uh oh!

boegelbot commented Feb 13, 2025

Uh oh!

verdurin commented Feb 13, 2025

Uh oh!

branfosj commented Feb 15, 2025

Uh oh!

branfosj commented Feb 15, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

github-actions Bot commented Feb 13, 2025 •

edited

Loading

Updated software `libStatGen-1.0.15-GCCcore-12.3.0.eb`

Updated software `Minimac4-4.1.6-GCC-12.3.0.eb`

Updated software `savvy-2.1.0-GCC-12.3.0.eb`

Updated software `shrinkwrap-1.2.0-GCCcore-12.3.0.eb`