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

…asyconfigs into core-packages-JSC-part9

.gitignore

@@ -1,12 +1,15 @@
 .pydevproject
 .project
 LICENSE_HEADER
+*.eb.bak_*
 *.pyc
 *.pyo
 *.nja
+*.out
 build/
 dist/
 *egg-info/
+.venv/
 *.swp
 *.ropeproject/
 eb-*.log

RELEASE_NOTES

@@ -3,10 +3,43 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages,
+The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages,
 incl. 41 different (compiler) toolchains.
 
 
+v4.9.4 (22 September 2024)
+--------------------------
+
+update/bugfix release
+
+- added example easyconfig files for 14 new software packages:
+  - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008),
+    MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424),
+    xskillscore (#21351)
+- added additional easyconfigs for various supported software packages, including:
+  - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0,
+    GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43,
+    GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4,
+    LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0,
+    NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0,
+    protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1,
+    scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2,
+    VirtualGL 3.1.1, zlib-ng 2.2.1
+- minor enhancements, including:
+  - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056)
+  - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337)
+- various bug fixes, including:
+  - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419)
+  - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429)
+  - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434)
+  - fix repeated sanity check runs in manta easyconfigs (#21435)
+  - fix test_easyconfig_locations when easyconfigs index is present (#21394)
+  - use proper dependency for libnsl in git-annex (#21441)
+  - avoid writing into ~/.stack directory during build for git-annex (#21452)
+- other changes:
+  - remove exts_default_options from TensorFlow 2.3.1 (#21290)
+
+
 v4.9.3 (14 September 2024)
 --------------------------
 

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb

@@ -0,0 +1,41 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'Tarball'
+
+name = 'ABRicate'
+version = '1.0.0'
+
+homepage = 'https://github.com/tseemann/abricate'
+description = "Mass screening of contigs for antimicrobial and virulence genes"
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+# https://github.com/tseemann/abricate
+github_account = 'tseemann'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('any2fasta', '0.4.2'),
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.14.1'),
+]
+
+postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']
+
+sanity_check_paths = {
+    'files': ['bin/abricate', 'bin/abricate-get_db'],
+    'dirs': ['db'],
+}
+
+sanity_check_commands = [
+    "abricate --help",
+    "abricate --list",
+]
+
+modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb

@@ -0,0 +1,41 @@
+easyblock = 'CMakeMake'
+
+name = 'ALL'
+version = '0.9.2'
+
+homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing'
+description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic
+domain-based load balancing into particle based simulation codes. The library
+is developed in the Simulation Laboratory Molecular Systems of the Jülich
+Supercomputing Centre at Forschungszentrum Jülich."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"]
+sources = ['loadbalancing-v%(version)s.tar.gz']
+checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Boost', '1.83.0'),  # only needed for tests
+]
+
+dependencies = [
+    ('VTK', '9.3.0'),
+]
+
+configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON '
+configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK '
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': [
+        'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod',
+        'lib/libALL.a', 'lib/libALL_fortran.a'
+    ],
+    'dirs': ['lib/cmake'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb

@@ -0,0 +1,41 @@
+easyblock = 'MakeCp'
+
+name = 'AMRFinderPlus'
+version = '3.12.8'
+
+homepage = 'https://github.com/ncbi/amr'
+description = """This software and the accompanying database are designed to find acquired antimicrobial
+ resistance genes and some point mutations in protein or assembled nucleotide sequences."""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+github_account = 'ncbi'
+source_urls = ['https://github.com/ncbi/amr/archive/']
+sources = ['amrfinder_v%(version)s.tar.gz']
+checksums = ['a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0']
+
+dependencies = [
+    ('BLAST+', '2.14.1'),
+    ('HMMER', '3.4'),
+    ('cURL', '8.0.1')
+]
+
+# Binaries are installed to the root of the installation, so add that root to the PATH:
+modextrapaths = {'PATH': ''}
+
+# a list of binary files that will be produced
+local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check',
+                  'fasta_extract', 'gff_check']
+
+files_to_copy = local_binaries
+
+sanity_check_paths = {
+    'files': local_binaries,
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    ('amrfinder', '-h')
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb

@@ -0,0 +1,29 @@
+name = 'AOCC'
+version = '4.2.0'
+
+homepage = 'https://developer.amd.com/amd-aocc/'
+description = """AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages. 
+ It supports target-dependent and target-independent optimizations. It is highly optimized for x86 targets, 
+ especially for AMD “Zen”-based processors giving a performance edge for time critical HPC and other 
+ applications over other compilers."""
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [
+    'https://download.amd.com/developer/eula/%(namelower)s/%(namelower)s-%(version_major)s-%(version_minor)s'
+]
+sources = ['%(namelower)s-compiler-%(version)s.tar']
+checksums = ['ed5a560ec745b24dc0685ccdcbde914843fb2f2dfbfce1ba592de4ffbce1ccab']
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.12.7'),
+]
+
+clangversion = '16.0.3'
+
+moduleclass = 'compiler'

easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb

@@ -0,0 +1,24 @@
+name = 'AOCC'
+version = '5.0.0'
+
+homepage = 'https://developer.amd.com/amd-aocc/'
+description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0"
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = ['https://download.amd.com/developer/eula/aocc/aocc-5-0/']
+sources = ['aocc-compiler-%(version)s.tar']
+checksums = ['966fac2d2c759e9de6e969c10ada7a7b306c113f7f1e07ea376829ec86380daa']
+
+clangversion = '17.0.6'
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.13.4'),
+]
+
+moduleclass = 'compiler'

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

@@ -0,0 +1,74 @@
+# Updated by: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'AUGUSTUS'
+version = '3.5.0'
+
+homepage = 'https://bioinf.uni-greifswald.de/augustus/'
+description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'Gaius-Augustus'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686']
+
+builddependencies = [
+    ('Python', '3.11.3'),
+]
+
+dependencies = [
+    ('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', '7.1.0'),
+    ('BamTools', '2.5.2'),
+    ('SQLite', '3.42.0'),
+]
+
+skipsteps = ['configure']
+
+# run "make clean" to avoid using binaries included with the source tarball
+prebuildopts = "make clean && "
+
+_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"'
+
+buildopts = ' '.join([
+    'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ',
+    _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'),
+    _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'),
+    _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'),
+])
+
+preinstallopts = "sed -i '/ln -sf/d' Makefile && "
+installopts = 'INSTALLDIR=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch',
+              'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes',
+              'bin/load2sqlitedb', 'bin/prepareAlign'],
+    'dirs': ['config', 'scripts'],
+}
+sanity_check_commands = ['augustus --help']
+
+modextrapaths = {'PATH': 'scripts'}
+modextravars = {
+    'AUGUSTUS_BIN_PATH': '%(installdir)s/bin',
+    'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config',
+    'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts',
+}
+
+moduleclass = 'bio'