Merge pull request #18279 from easybuilders/4.8.x

release EasyBuild v4.8.0

Author: boegel

.github/workflows/unit_tests.yml

@@ -13,10 +13,10 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.6]
+        python: [3.6]
         modules_tool: [Lmod-7.8.22, Lmod-8.6.8]
         module_syntax: [Lua, Tcl]
-        # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 2.7 & 3.6
+        # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6
         exclude:
           - modules_tool: Lmod-7.8.22
             module_syntax: Tcl
@@ -34,7 +34,7 @@ jobs:
         key: eb-sourcepath
 
     - name: set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{matrix.python}}
         architecture: x64
@@ -159,12 +159,12 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.6, 3.7]
+        python: [3.6]
     steps:
     - uses: actions/checkout@v2
 
     - name: set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{matrix.python}}
 

RELEASE_NOTES

@@ -3,10 +3,95 @@ 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 17,098 easyconfig files, for 3,085 different software packages,
+The latest version of easybuild-easyconfig provides 17,511 easyconfig files, for 3,161 different software packages,
 incl. 39 different (compiler) toolchains.
 
 
+v4.8.0 (7 Jul 2023)
+--------------------
+
+feature release
+
+- added easyconfigs for foss/2023a (#18264) and intel/2023a (#18275) common toolchains
+- added example easyconfig files for 76 new software packages:
+  - 3d-dna (#9258), affinity (#18051), AIMAll (#13153), alleleIntegrator (#17923), AlphaPulldown (#17774),
+    ASCAT (#17923), ASF-SearchAPI (#18179), ATAT (#18213), AutoDockSuite (#9678), axel (#10961), BayesPrism (#17885),
+    BGC-Bayesian-genomic-clines (#18005), CalculiX-CrunchiX (#16805), CASA (#18055), cctbx-base (#17774),
+    Circuitscape (#16720), CppHeaderParser (#18272), CuCLARK (#9482), cuteSV (#18077), DALI (#18204), DaliLite (#17989),
+    DEICODE (#18181), dm-haiku (#18013), dominate (#18086), dx-toolkit (#18232), easel (#18156), ecFlow (#15719),
+    EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170),
+    HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073),
+    mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198),
+    NanoStat (#18201), oxDNA (#18175 + #18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951),
+    plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180),
+    pyMannKendall (#18044), pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086),
+    PyTorch-Image-Models (#18220), PyWBGT (#17980), Safetensors (#18220), Sniffles (#18048), strace (#14381),
+    Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), SVIM (#18071), Tapenade (#18109),
+    TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), visdom (#18086),
+    wrapt (#18125), xclip (#17055), xdotool (#17055)
+- added additional easyconfigs for various supported software packages, including:
+  - AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0,
+    boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10,
+    corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1,
+    datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3,
+    elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2,
+    FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1,
+    Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1,
+    hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2,
+    Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0,
+    lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1,
+    minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3,
+    Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2,
+    OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1,
+    PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6,
+    pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3,
+    python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4,
+    seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0,
+    tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0,
+    UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2,
+    XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7
+- minor enhancements, including:
+  - add CI check for -DCMAKE_BUILD_TYPE, should use build_type instead (#14008)
+  - enhance sanity check for recent LibTIFF easyconfigs (#17975)
+  - update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module (#17982)
+  - use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167)
+  - update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173)
+  - add extra packages to recent R easyconfigs (#18029, #18063, #18122, #18195, #18245)
+  - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18196, #18246)
+- various bug fixes, including:
+  - add patches to fix TensorFlow 2.7.1 on POWER (#16795)
+  - fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ foss/2021b (#17058)
+  - stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998)
+  - add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007)
+  - fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030)
+  - update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies (#18041)
+  - fix --sanity-check-only for MAGeCK v0.5.9.4 (#18047)
+  - enable building static libs and check for libexslt.* in libxslt (#18064)
+  - add -pthread flag for dorado (#18072)
+  - add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 (#18087)
+  - add missing pkgconf build dependency for XML-LibXML v2.0208 (#18159)
+  - update homepage for NWChem 7.x (#18184)
+  - update homepage for SUNDIALS 5.x and 6.x (#18186)
+  - add missing source_urls for SimpleITK (#18212)
+  - use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (#18230)
+  - fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231)
+  - fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235)
+  - use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236)
+  - update source_urls for Velvet 1.2.10 (#18237)
+  - use upstream patch for symbol compatibility in XZ 5.2.5 (#18250)
+  - update source url for pkgconf (#18271)
+- other changes:
+  - stop running easyconfig unit tests with Python 2.7 (#18006)
+  - fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b) (#18061)
+  - remove unused PyTorch patch (#18062)
+  - allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098)
+  - bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188)
+  - remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222)
+  - remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223)
+  - remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260)
+  - change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a) (#18263)
+
+
 v4.7.2 (27 May 2023)
 --------------------
 
@@ -99,6 +184,7 @@ update/bugfix release
   - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775)
   - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869)
 
+
 v4.7.1 (March 20th 2023)
 ------------------------
 

easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb

@@ -0,0 +1,35 @@
+easyblock = 'Tarball'
+
+name = '3d-dna'
+version = '180922'
+versionsuffix = '-Python-%(pyver)s'
+local_githash = '529ccf46599825b3047e58a69091d599e9858a19'
+
+homepage = 'https://github.com/theaidenlab/3d-dna'
+description = """3D de novo assembly (3D DNA) pipeline"""
+
+toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+
+source_urls = ['https://github.com/theaidenlab/%(name)s/archive']
+sources = [{'download_filename': '%s.zip' % local_githash, 'filename': SOURCE_ZIP}]
+checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca']
+
+dependencies = [
+    ('Python', '2.7.15'),
+    ('LASTZ', '1.02.00'),
+    ('Java', '1.8', '', SYSTEM),
+    ('parallel', '20190622'),
+]
+
+postinstallcmds = ['chmod 755 %(installdir)s/*.sh']
+
+sanity_check_paths = {
+    'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["run-asm-pipeline.sh --help"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb

@@ -0,0 +1,59 @@
+#
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.2.1'
+
+homepage = 'https://www.abinit.org/'
+description = """ABINIT is a package whose main program allows one to find the total energy,
+ charge density and electronic structure of systems made of electrons and nuclei (molecules
+ and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a
+ planewave or wavelet basis."""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0']
+
+builddependencies = [
+    ('Python', '3.7.4'),
+]
+dependencies = [
+    ('libxc', '4.3.4'),
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
+    ('HDF5', '1.10.5'),
+]
+
+# Ensure MPI.
+configopts = '--with-mpi="yes" --enable-openmp="no" '
+
+# BLAS/Lapack
+configopts += '--with-linalg-flavor="openblas"  LINALG_LIBS="-L${EBROOTOPENBLAS}/lib -lopenblas" '
+
+# FFTW3 support
+configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# make sure --free-line-length-none is added to FCFLAGS
+configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" '
+
+# `make check` is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb

@@ -0,0 +1,57 @@
+#
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.2.1'
+
+homepage = 'https://www.abinit.org/'
+description = """ABINIT is a package whose main program allows one to find the total energy,
+ charge density and electronic structure of systems made of electrons and nuclei (molecules
+ and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a
+ planewave or wavelet basis."""
+
+toolchain = {'name': 'intel', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0']
+
+builddependencies = [
+    ('Python', '3.7.4'),
+]
+dependencies = [
+    ('libxc', '4.3.4'),
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
+    ('HDF5', '1.10.5'),
+]
+
+# Ensure MPI with intel wrappers.
+configopts = '--with-mpi="yes" --enable-openmp="no" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# BLAS/Lapack from MKL
+configopts += '--with-linalg-flavor=mkl '
+
+# FFTW from MKL
+configopts += '--with-fft-flavor=dfti '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# `make check` is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb

@@ -0,0 +1,69 @@
+# easybuild easyconfig
+#
+# John Dey <jfdey@fredhutch.org> Fred Hutchinson Cancer Center
+# Thomas Eylenbosch - Gluo NV
+#
+easyblock = 'Bundle'
+
+name = 'AGAT'
+version = '1.1.0'
+
+homepage = 'https://agat.readthedocs.io/en/latest/'
+description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations
+ in any GTF/GFF format."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('BioPerl', '1.7.8'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perl -e 'require %(ext_name)s'", '')
+
+exts_list = [
+    ('Set::Object', '1.42', {
+        'source_tmpl': 'Set-Object-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'],
+        'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'],
+    }),
+    ('File::Share', '0.27', {
+        'source_tmpl': 'File-Share-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'],
+    }),
+    ('Sort::Naturally', '1.03', {
+        'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'],
+    }),
+    ('Class::MethodMaker', '2.24', {
+        'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'],
+        'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'],
+    }),
+    ('Term::ProgressBar', '2.23', {
+        'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'],
+    }),
+    (name, version, {
+        'modulename': 'AGAT::Utilities',
+        'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002'],
+    }),
+]
+
+modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'],
+}
+
+sanity_check_commands = ['agat_convert_bed2gff.pl --help']
+moduleclass = 'bio'