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RELEASE_NOTES
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This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
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 17,511 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)
--------------------
update/bugfix release
- added easyconfigs for intel/2023.03 (#17676)
- added example easyconfig files for 89 new software packages:
- AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833),
BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736),
CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751),
CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591),
ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635),
GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833),
HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928),
libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913),
MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496),
PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397),
py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626),
python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968),
Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472),
sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851),
spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553),
Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606),
WCSLIB (#15497), ZIMPL (#17639)
- added additional easyconfigs for various supported software packages, including:
- Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21,
Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1,
bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11,
Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1,
CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0,
Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0,
freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4,
googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0,
Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5,
L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1,
libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12,
libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4,
libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6,
mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4,
netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0,
Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1,
pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0,
pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0,
pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01,
ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4,
ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1,
ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0,
Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0,
Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5
- minor enhancements, including:
- add local::lib extension to Perl 5.34.0 (#17679)
- install shared libraries for tesseract (#17721)
- add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738)
- add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852)
- add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852)
- various bug fixes, including:
- add patch for UCC 1.1.0 for multiple component paths (#17255)
- fix configure step for ELSI 2.5.0+ (#17288)
- switch bamtofastq to Cargo easyblock (#17595)
- add missing OpenJPEG dependency for recent GDAL versions (#17599)
- fix CodAn bin/* executable permissions for all users #(#17607)
- upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612)
- add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618)
- add alternative checksum for MONAI 1.0.1 (#17628)
- fix paths to Perl modules in MAKER v3.01.04 (#17629)
- add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631)
- explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638)
- remove LLVM build dependency from TensorFlow easyconfigs (#17641)
- update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666)
- fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697)
- add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713)
- use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717)
- exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737)
- add missing PCRE dependency for InterProScan 5.55-88.0 (#17762)
- fix building Python bindings of DGL, requires static libs (#17764)
- only use QEF gitlab source url for QuantumESPRESSO itself (#17766)
- add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779)
- fix broken source URL for AOCC 4.0.0 (#17794)
- specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830)
- add Doxygen build dependency to X11 (#17842)
- FLINT needs BLAS so move it up from GCC level (#17868)
- fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875)
- add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887)
- add historical repo paths to install cmd for old versions of texlive (#17893)
- add missing FastTreeMP binary for FastTree (#17897)
- add checksum for arm64 source tarball for Go 1.18.3 (#17903)
- add patch to fix test_quantization in PyTorch 1.12.1 (#17908)
- add make 4.3 as build dependency for recent OpenBLAS versions (#17924)
- other changes:
- 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)
------------------------
update/bugfix release
- added example easyconfig files for 99 new software packages:
- astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940),
CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326),
cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225),
DensPart (#17473), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497),
eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271),
finder (#1917), flowFDA (#17495), gbasis (#17473), genomepy (#17506), Giotto-Suite (#17207), GKeyll (#16044),
GraphDB (#17280), graphviz-python (#17352), grid (#17473), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341),
HiCMatrix (#17330), Inferelator (#17223), iodata (#17473), irodsfs (#17486), jupyter-contrib-nbextensions (#17270),
jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267),
krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAKER (#17345),
methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524),
Parallel-Hashmap (#17311), pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275),
PLAMS (#17473), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150),
pytest-rerunfailures (#17295), pytest-shard (#17295), python-louvain (#17207), PyTorch-Ignite (#15491),
PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189),
scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), silhouetteRank (#17207),
siscone (#17342), smfishHmrf (#17207), sparse-neighbors-search (#17329), SpatialDE (#17207), sradownloader (#17188),
stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371),
vitessce-python (#17472), vitessceR (#17525), YODA (#17343)
- added additional easyconfigs for various supported software packages, including:
- AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0,
BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1,
Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0,
Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8,
CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6,
DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0,
FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4,
GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1,
googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1,
h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2,
Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0,
imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5,
JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2,
Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0,
libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0,
MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2,
Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14,
mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1,
networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0,
OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0,
PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0,
presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2,
py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0,
PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1,
QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1,
ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0,
SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0,
snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1,
SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3,
Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only,
Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226,
Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6
- minor enhancements, including:
- add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523)
- add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494)
- add sanity check command to OpenMolcas v22.10 (#17128)
- add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151)
- add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159)
- enhance OpenFold 1.0.1 for standalone usage (#17206)
- add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213)
- set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216)
- add Devel::Size + Math::Utils extension to recent Perl easyconfigs (#17246, #17466)
- combine errors of extension patch check into a single failure (#17286)
- add case-insensitive name clash test (#17303)
- add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316)
- use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429)
- add source URL to cuDNN 8.8 easyconfig (#17439)
- add missing zstd dep to Boost (#17482)
- various bug fixes, including:
- fix postinstallcmds and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740)
- fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845)
- add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077)
- fix build of TensorFlow 2.5+ on aarch64 (#17101)
- explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129)
- add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135)
- add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140)
- fix source URL for p7zip v17.x (#17144)
- add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165)
- remove dependency on Pillow from scikit-bio v0.5.7 (#17178)
- correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204)
- use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221)
- fix CMake print summary for long hostnames for NECI (#17230)
- add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240)
- include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242)
- add patch for PAPI 7.0.0 to fix compilation error (#17244)
- also update $PERL5LIB for RepeatMasker v4.1.4 (#17245)
- add alternative source_url for MariaDB > 10.4 (#17250)
- remove use of rysnc in building Kent_tools (#17252)
- add missing pkgconf build dependency in recent libxslt easyconfigs (#17254)
- add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (#17257)
- fix postinstallcmds in shovill easyconfigs (#17279)
- allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289)
- remove duplicate SlamDunk easyconfig using lowercase name (#17301)
- use https in homepage + source URL for GenomeThreader 1.7.3 (#17338)
- consistently use Check capitailisation (#17351)
- add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (#17356)
- fix homepage + source URL for ELPA (due to switch to new domain) (#17357)
- fix homepage in ELPA easyconfigs (due to switch to new domain) (#17358)
- rename libpsml for consistency with libPSML (#17359)
- replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs (#17412)
- update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (#17413)
- add patch for Qt5 5.12.2 with GCCcore/11.2.0 to fix template bug (#17464)
- replace src include path with installation dir for HDF5 (#17469, #17488)
- disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (#17499)
- update homepage and source urls of DFT-D3 (#17528)
- use Binary easyblock for ANIcalculator to prevent RPATH sanity check failures (#17536)
- other changes:
- fix invalid escape sequences in easyconfigs by using raw strings (r"...") (#11149)
- add exception for ncbi-vdb 3.0.0 dependency variant (#17131)
- use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (#17167)
- enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196)
- fix website/docs links in README (#17232)
- remove commented out line and delete unused patch for TALON (#17298)
- re-enable disabled tests (#17304)
- rename MAGMA to MAGMA-gene-analysis to avoid name collision (#17345)
- Archive ARB and blasr patch files (#17346)
- Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348)
- consistently use NanoFilt capitalisation (#17349)
- rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350)
- rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352)
- archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364)
4.7.0 (Janurary 9th 2023)
-------------------------
feature release
- added easyconfigs for foss/2022b, intel/2022b common toolchains (#16961 and #16962)
- see also https://docs.easybuild.io/en/latest/Common-toolchains.html
- added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724)
- added example easyconfig files for 107 new software packages:
- Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757),
captum (#16477), CAT-BAT (#16577, #16634), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842),
CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749),
cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391),
DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704),
ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853),
HyperQueue (#16753), IJulia (#16494, #16665), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844),
KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088),
Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911),
minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892, #17029),
MultilevelEstimators (#15630, #16665), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751),
nf-core-mag (#16613), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564),
Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576),
PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447),
resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032),
SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027),
Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048),
TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587),
torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637)
- added additional easyconfigs for various supported software packages, including:
- Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1,
basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a,
boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8,
CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2,
cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1,
dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1,
FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20,
Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0,
git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35,
HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2,
ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0,
libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0,
libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1,
LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3,
libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4,
MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1,
MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1,
nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2,
Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7,
OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0,
OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4,
phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3,
pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3,
Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5,
QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1,
rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3,
scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0,
SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007,
SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0,
texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0,
typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2,
wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0,
XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6
- minor enhancements, including:
- enable building of dev tools in recent PyQt5 easyconfigs (#16469)
- add extensions to R v4.2.1: LMERConvenienceFunctions (#16512), HGNChelper 4.2.1 (#16744)
- add extensions to R-bundle-Bioconductor 3.15: SPOTlight (#16569), HiCcompare (#16581), ROntoTools (#16636),
scDblFinder (#16686), numbat (#16777), HiCBricks (#16913), zellkonverter (#16952)
- add libmad dependency to SoX v14.4.2 (#16758)
- also install subtree support in recent git easyconfigs (#16784, #16785)
- add extensions to ESM-2 to enhance it for esmfold (#16841)
- add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844)
- add KaHIP dependency to OpenFOAM v2206 (#16974)
- enable dataset support for recent versions of Arrow (#16956)
- various bug fixes, including:
- define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776)
- add patches to fix PyTorch 1.10.0 build on POWER (#15904)
- fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485)
- add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility (#16486)
- add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (#16487)
- work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (#16490)
- fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (#16502)
- add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot (#16510)
- add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (#16516)
- build nodejs with OpenSSL and ICU provided as proper dependencies (#16529)
- also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs (#16556)
- define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (#16570)
- disable use of -Werror in recent NSS easyconfigs (#16571)
- use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (#16611)
- avoid that zlib + htslib are downloaded and built during installation of MetaBAT (#16624)
- add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (#16633)
- add missing pyWannier90 dependency for mcu + enhance sanity check (#16667)
- fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (#16693)
- add patches to fix or skip PyTorch 1.12.1 tests (#16793)
- fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (#16819)
- upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (#16839)
- fix checksum for dlllogger extension in OpenFold v1.0.0 (#16694)
- make sure that Python dependency is actually used for VTK 9.0.1 (#16741)
- fix homepage for pocl v1.8 (#16857)
- fix source_urls in MUMPS easyconfigs (#16931, #16932)
- fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (#16946)
- add missing OpenSSL dependency to DCMTK 3.6.7 (#16979)
- fix source URL for PCRE2 (#16987)
- add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (#16990)
- add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (#17001)
- add missing zlib and zstd to GnuTLS (#17013)
- add missing pkgconf build dependency to Transformers v4.24.0 (#17020)
- fix checksums for xxx-rocm-4.5.0.tar.gz source tarballs for Clang-AOMP 4.5.0 (#17042)
- replace useless test step for simint 0.7 with (lightweight) sanity check command (#17044)
- other changes:
- only give read permissions in GitHub Actions workflows (#16263)
- remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (#16492)
- include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (#16578)
- use new EasyBuild logo in README (#16641)
- rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (#16697)
- automatically cancel Github Action workflow runs for outdated commits (#16754)
- use geo moduleclass for SimPEG 0.14.1 (#16847)
4.6.2 (October 21st 2022)
-------------------------
update/bugfix release
- add easyconfig for intel/2022.09 toolchain (#16435)
- added example easyconfig files for 25 new software packages:
- AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436),
Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16082, #16319), f90wrap (#16346),
Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254),
pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428),
TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163)
- added additional easyconfigs for various supported software packages, including:
- Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3,
dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2,
GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6,
Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30,
libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0,
NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0,
OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4,
PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1,
scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0,
sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0,
TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107,
VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5
- minor enhancements, including:
- configure recent pocl versions with -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246)
- add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316)
- enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406)
- add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422)
- add AMAPVox extension to R v4.2.1 (#16439)
- add OpenEXR depenency to POV-Ray 3.7.0.10 (#16408)
- various bug fixes, including:
- add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199)
- skip flaky test in PyTorch 1.9.0 (#16258)
- add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270)
- add missing pkg-config build dependency to Guile (#16317)
- add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332)
- add patches to fix PyTorch 1.11 on POWER (#16339)
- add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (#16343)
- use Intel MPI from EasyBuild toolchain in AMS (#16363)
- fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383)
- fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396)
- fix GitHub download link in for libpsl 0.21.1 (#16397)
- stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403)
- add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407)
- add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410)
- add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411)
- fix checksum for GULP 6.1 (#16423)
- add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450)
- other changes:
- drop Java dep from ABAQUS 2022 (#16314)
- deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384)
- update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386, #16418)
- update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429)
v4.6.1 (September 12th 2022)
----------------------------
update/bugfix release
- added example easyconfig files for 37 new software packages:
- AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#15883, #16210),
FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071),
how_are_we_stranded_here (#16220, #16227), indicators (#16209), JavaFX (#8583), json-fortran (#15979),
jupyter-resource-usage (#15834), libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047),
MetaMorpheus (#15825), mgltools (#16226), miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097),
olaFlow (#16021), OpenFAST (#15983, #15983), OpenFold (#15971), Phantompeakqualtools (#15871),
pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), Satsuma2 (#16068), SMC++ (#16017), stripy (#15866),
UCC-CUDA (#15956), VESTA (#16217)
- added additional easyconfigs for various supported software packages, including:
- alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39,
BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5,
CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1,
Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2,
GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8,
glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2,
HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1,
libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1,
maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2,
MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1,
ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0,
pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2,
PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0,
scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62,
Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0,
Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0
- minor enhancements, including:
- add alternate download URL for Voro++ (#15898)
- add extra symlinks and sanity checks for libtinfo in ncurses (#15903)
- include some easyconfig constants in flake8 configuration file (#16040)
- add pigz dependency for cutadapt v3.4 + v3.5 (#16056)
- add sanity check commands for recent gettext versions (>= 0.20.x) (#16091)
- various bug fixes, including:
- use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (#13375)
- fix set-alias statements for MaxQuant v2.0.3.0 (#15743)
- add Autotools build dependency to R 4.2.0 w/ foss 2021b (#15822)
- add patch for BLIS to fix auto-detection of POWER (#15826)
- downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840)
- explicitly enable HDF5 from kallisto v0.46.2 onwards (#15843)
- add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (#15856)
- use build enviroment set by EasyBuild and add missing dependency on zlib to minimap2 (#15859)
- add missing dependencies and execute tests on Trycycler v0.5.2 (#15864)
- add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (#15874)
- exclude (flaky) fault_tolerance_test and fix non-x86 build for TensorFlow 2.7.1 (#15882)
- work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong (#15885)
- fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (#15889)
- add and fix patches for PyTorch 1.9.0 on POWER (#15919)
- exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (#15932)
- consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#15935, #16225)
- add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (#15968)
- refactor checksum test for extensions to use collect_exts_file_info (#15973)
- fix dependency on FOX Toolkit in SUMO (#15986)
- add missing SciPy-bundle dependency for rMATS-turbo (#15988)
- explictely download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#15993)
- restore ploteig in EIGENSOFT 7.2.1 (#15996)
- add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (#16011)
- add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (#16027) and 2021 (#16026)
- exclude failing test in TensorFlow 2.4.1 (#16042)
- skip NASA performance and remote server tests in netCDF v4.9.0 (#16050, #16158)
- use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option) (#16064)
- add patch to fix pkgconfig file for Blitz++ v1.0.2 (#16102)
- add missing BCFtools dependency for recent medaka versions (#16107)
- add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (#16112)
- fix checksum for Stacks v2.62 (due to silent re-release without version bump) (#16134)
- fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (#16145)
- fix top level Makefile for AmberTools 20 and enable tests (#16150)
- add missing patches + enable running tests for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152)
- replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153)
- remove modextrapaths to add top-level install directory to $PATH for recent InterProScan easyconfigs (now done by default by Binary easyblock) (#16167)
- fix sources + source URL + homepage for Molekel v5.4.0 (#16219)
- consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (#16231)
- fix checksum for CUDA 11.4.1 aarch64 installer (#16234)
- remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (#16238)
- add direct Pango dependency in recent ImageMagick easyconfigs (#16237)
- other changes:
- remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384)
- synchronize ncurses easyconfigs using system toolchain (#15903)
- stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (#15906)
- speed up OpenMPI 4.1.4 configure by not running "autogen.pl --force", but only running required Autotools commands (#15957)
- replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (#15958)
- simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (#15981)
- update Java/11 to 11.0.16 and Java/17 to 17.0.4 (#16001)
- remove unecessary patch in recent JupyterLab (#16030)
- update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#16070)
- make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant (#16126)
v4.6.0 (July 8th 2022)
----------------------
feature release
- added easyconfigs for foss/2022a, intel/2022a common toolchains (#15755)
- add easyconfig for gfbf/2022a toolchain (#15653, #15755)
- see also https://docs.easybuild.io/en/latest/Common-toolchains.html
- added example easyconfig files for 24 new software packages:
- BLT (#15624), category_encoders (#15638), fio (#10321), FSON (#15721), G-PhoCS (#7619), GCTA (#15649),
Gibbs2 (#15702), InterProScan_data (#15717), Jorg (#15346), libopus (#15682), Minipolish (#15713),
mm-common (#15764), MONA (#15696), NetPyNE (#15606), pfind (#15685), regionmask (#15786), samplot (#15686),
SISSO (#15766), sklearn-pandas (#15637), STAR-CCM+ (#7398), SWIPE (#6795), topaz (#15739),
uncertainty-calibration (#15612), Virtuoso-opensource (#14102)
- added additional easyconfigs for various supported software packages, including:
- AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6,
cppy 1.2.1, deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0,
gdbm 1.21, geopandas 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 4.0.3, GULP 6.1, h5py 3.7.0,
HDF5 1.13.1, hifiasm 0.16.1, IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, IRkernel 1.3,
jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17,
libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1,
LittleCMS 2.13.1, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 2.12.12, netCDF 4.9.0, nettle 3.8,
networkx 2.8.4, NEURON 7.8.2, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2,
Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0,
protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2,
Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, Ray-project 1.13.0, RE2 2022-06-01,
redis-py 4.3.3, ReFrame 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, Shapely 1.8.2, Siesta 4.1.5,
SimpleITK 2.1.1.2, SpectrA 1.0.1, TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1,
UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 3.9.1, Xvfb 21.1.3
- minor enhancements, including:
- add extensions to R v4.2.0: hypergeo (#15701), rtdists (#15734), geeM (#15810)
- add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (#15715)
- add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (#15730)
- various bug fixes, including:
- switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (#15636)
- avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (#15657)
- add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (#15691)
- correct configopts in deal.II v9.1.1 easyconfig (#15692)
- add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (#15694)
- other changes:
- disable flaky GPU test for TensorFlow 2.6.0 (#15824)
v4.5.5 (June 8th 2022)
----------------------
update/bugfix release
- add candidates for 2022a common toolchains: foss/2022.05 (#15561), intel/2022.05 (#15485)
- added example easyconfig files for 35 new software packages:
- Albumentations (#15302), AMPtk (#15435), arosics (#15249), CellTypist (#15530), detectron2 (#15442),
EigenExa (#15234), Fastaq (#15332), FFTW.MPI (#15561), FreeBarcodes (#15350), gcloud (#15443),
GST-plugins-bad (#15446), gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395),
libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito (#15314),
parameterized (#15481), purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065),
scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#14601), UCC (#14291),
Wayland (#11107), XGrafix (#15268), XPLOR-NIH (#15479)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317,
Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0,
breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0,
CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187,
EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6,
freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8,
geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0,
Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12,
HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3,
IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1,
libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1,
libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7,
libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0,
Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1,
mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2,
Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0,
OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1,
Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0,
PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0,
RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0,
SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1,
SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5,
tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0,
vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2
- minor enhancements, including:
- use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (#15227)
- also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (#15347)
- add extensions to R v4.1.2 + v4.2.0 easyconfigs:
- Hmsc (#15393), MonteCarlo + RhpcBLASctl (#15438), chkptstanr (#15540), chkptstanr + MLmetrics + renv (#15573)
- add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (#15405)
- use redist source_urls for cuDNN > 7.5 (#15411)
- add download_instructions to Java 1.8 > 200 (#15412)
- update Arrow to use EasyBuild-provided versions of some dependencies and enable all compression codecs (#15512)
- add csh -> tcsh symlink in recent tcsh easyconfigs (#15571)
- allow external tools to be located elsewhere for ETE (#15578)
- add additional sanity check commands for IQ-TREE v2.2.1 (#15596)
- various bug fixes, including:
- fix source URL for freetype 2.6.5 with foss/2016b (#14204)
- fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (#15206)
- use x.py to boostrap Rust so that build options are properly passed through (#15211)
- fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15280, #15615)
- add hwloc dependency to tbb v2021.4.0 (#15294)
- tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313)
- remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316)
- update source URL for isl in GCCcore easyconfigs (#15320)
- update source URLs for YAXT 0.9.x to fix download (#15323)
- define $HHLIB as path to HH-suite installation directory, required by Perl scripts (#15324)
- add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, #15381)
- add missing dependencies for libheif (libpng, libjpeg-turbo) (#15408)
- switch to configuring build of libheif with CMake so libde265 dependency is picked up (#15408)
- disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b (#15495)
- add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528, #15589)
- add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (#15566)
- also build shared library + fix $PYTHONPATH for gmsh 4.9.0 (#15579)
- add patch for GLib 2.68.2 to fix use of close_range (#15594)
- fix download of thrift 0.12.0 for Arrow 0.16.0 (#15597)
- add Bison and flex build dependencies to SCOTCH 6.1.x (#15618)
- add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (#15619)
- add missing dependencies + switch to non-static build for Arriba v2.1.0 (#15623)
- other changes:
- add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (#15216)
- update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (#15592)
- install sklearn meta-package with scikit-learn v1.0.1 (#15613)
- switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616, #15617)
v4.5.4 (March 31st 2022)
------------------------
update/bugfix release
- added example easyconfig files for 29 new software packages:
- Abseil (#15102), AMS (#13155), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#15052),
Devito (#14984, #15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844),
M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174),
ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035),
porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050),
STRique (#14980), XML-Compile (#15177)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1,
CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0,
ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0,
IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0,
KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a,
MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2,
NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3,
parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1,
RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3,
VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0
- minor enhancements, including:
- add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (#15027)
- add check to verify that patch files touched in PRs have a description in place (#15061)
- add extensions to R v4.1.2 easyconfig: hash (#15098), nabor + harmony (#15117), apluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps (#15141)
- also install rMATS_P commands in rMATS-turbo easyconfig (#15113)
- add extensions to Bioconductor v3.14 easyconfig: chromVAR (#15118), EnsDb.Hsapiens.v79 (#15154), WGCNA (#15178)
- add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (#15176), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (#15190)
- enable running of tests for MEME with gompi/2021b (#15191, #15199)
- various bug fixes, including:
- add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (#14847)
- downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (#14942)
- add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (#14987), optmatch (#14993)
- avoid pollution in the tmp directory when running the AlphaFold tests (#14989)
- consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (#15039)
- fix GBprocesS easyconfig by switching to source tarball created using git_config (#15048)
- add patches for mauveAligner to fix build on RHEL8 (#15049)
- fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (#15051)
- add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (#15054)
- avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (#15055)
- fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 (#15059)
- don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (#15060)
- add M4 as build dependency for CCL-1.12 (#15075)
- configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults (#15086)
- set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (#15097)
- remove disable flag for RTTI in snappy v1.1.9 (#15099)
- fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (#15121)
- clean up PSolver and futile easyconfigs and add dynamic libs (#15148)
- enhance vcflib easyconfigs to also install scripts (#15181)
- add patch to fix shared linking in vcflib (#15203)
- fix failing sanity check for PRINSEQ (#15205)
- other changes:
- use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (#15003)
- disable building of documentation for DBus 1.13.18 (#15010)
- consistently use system toolchain in EasyBuild easyconfigs (#15126)
- use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (#15149)
v4.5.3 (February 11th 2022)
---------------------------
update/bugfix release
- added example easyconfig files for 25 new software packages:
- Arcade-Learning-Environment (#14753), Bambi (#14811), CASTEP (#14420), Crumble (#14785), deepmedic (#14953),
FoBiS (#14771), histolab (#14945), Iris (#14788), Jasmine (#14789), libexif (#14823), libgdiplus (#14823),
MuJoCo (#14965), mujoco-py (#14776, #14965), namedlist (#14814), OpenCensus-python (#14837), PyEVTK (#14911),
pyradiomics (#14851), PyTorch-Lightning (#14933), Redis (#14783), rising (#14952), SoXt (#14803),
SURVIVOR (#14786), tensorboard (#14926), xtensor (#14944), xxd (#14846)
- added additional easyconfigs for various supported software packages, including:
- aiohttp 3.8.1, AOCC 3.2.0, ArviZ 0.11.4, BeautifulSoup 4.10.0, bokeh 2.4.2, Boost.Python 1.77.0,
Bowtie 1.3.1, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.5.1, ConnectomeWorkbench 1.5.0, Crumble 0.8.3,
CUDA 11.5.1 + 11.6.0, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepTools 3.5.0, dm-tree 0.1.6,
DROP 1.1.1, ecCodes 2.24.2, Emacs 27.2, FDS 6.7.7, file 5.41, Flask 2.0.2, FORD 6.1.6, GATE 9.1,
Geant4 11.0.0, GEMMA 0.98.5, GnuTLS 3.7.3, Go 1.17.6, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5,
Guile 3.0.7, HDF5 1.10.8, imageio 2.13.5, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libpsml 1.1.10,
libRmath 4.1.2, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, likwid 5.2.1, MaxQuant 2.0.3.0,
MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, Mono 6.12.0.122, MUSCLE 5.1,
nanomax-analysis-utils 0.4.3, ncbi-vdb 2.11.2, NCIPLOT-4.0 20200624, Nextflow 21.10.6, NGS 2.11.2,
nvtop 1.2.2, OpenCV 4.5.5, openslide-python 1.1.2, pftoolsV3 3.2.11, picard 2.26.10, pydicom 2.2.2,
pyFAI 0.20.0, Pysam 0.18.0, pytest-xdist 2.5.0, Racon 1.5.0, RAxML 8.2.12, ReFrame 3.10.1, ROOT 6.24.06,
scikit-image 0.19.1, SDL2 2.0.20, SeqKit 2.1.0, Siesta 4.1.5, SimpleITK 2.1.1, SqueezeMeta 1.5.0,
tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing-extensions 3.10.0.2
- minor enhancements, including:
- also install Python bindings for SHTns 3.5.1 (#14893)
- add catlearn extension to easyconfig for R v4.1.2 (#14940)
- various bug fixes, including:
- update TALYS sources to (hopefully) ensure constant checksums (#14797)
- add missing graphite2 + HarfBuzz dependencies to Qt5 v5.15.2 (#14802)
- add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 (#14859)
- specify easybuild.io as EasyBuild homepage in setup.py (#14870)
- add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 (#14873) and R 4.1.2 (#14880) easyconfigs
- add patch to fix Kraken2 ncbi ftp/https check in rsync_from_ncbi.pl for versions 2.0.9-2.1.1 (#14889)
- disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build (#14923)
- disable use of -Werror for recent NSS versions (#14924)
- fix download URL in UDUNITS v2.2.28 easyconfigs (#14954)
- remove unnecessary CUDAcore dependency from nvtop v1.2.1 easyconfig (#14957)
- consistently apply patch for mapDamage 2.2.1 to use external seqtk (#14961)
- fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: $(name)s should be %(name)s (#14962)
- other changes:
- update Java/17 wrapper to Java 17.0.2 (#14868)
- use actions/setup-python@v2 in CI workflows + trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (#14857, #14881)
v4.5.2 (January 24th 2022)
--------------------------
update/bugfix release
- added easyconfig for intel/2022.00 toolchain (#14620)
- added example easyconfig files for 48 new software packages:
- alevin-fry (#14617), AMD-uProf (#14626), ANGEL (#11857), atropos (#7580), Austin (#14596), AutoDock-GPU (#14671),
AutoDock-Vina (#14675), boost_histogram (#14516), CAFE5 (#14603), Calcam (#7488), Carma (#14527), Cogent (#14278),
dlib (#14556), DualSPHysics (#14632), dune-core (#14693), dune-fem (#14693), DyMat (#14615), elbencho (#14548),
Embree (#7471), ExaML (#14530), FMPy (#14481), genozip (#14583), hivtrace (#14691), intervaltree-python (#8995),
IsoNet (#14075), MACSE (#14709), MetaPhlAn (#12917), MicrobeAnnotator (#14549), mold (#14595), numdiff (#14609),
OpenFace (#14556), PhyloPhlAn (#14564), PREQUAL (#14722), PuLP (#14581), PyCalib (#14616), PyTorch3D (#13240),
QCG-PilotJob (#14337), RaGOO (#8995), RAPSearch2 (#13199), SCopeLoomR (#14518), ShengBTE (#14557), SHTns (#14682),
STRUMPACK (#14560), TALYS (#14716), TN93 (#14691), xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516)
- added additional easyconfigs for various supported software packages, including:
- annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0,
cDNA_Cupcake 26.0.0, CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, dotNET-Core-Runtime 6.0.1,
dotNET-SDK 6.0.101, Extrae 3.8.3, fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, GTK3 3.24.31,
h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2,
libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428,
numba 0.54.1, NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 3.4.1, OpenFOAM v2112, ORCA 5.0.2,
phonopy 2.12.0, Pillow 8.3.2, Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 0.12.3,
python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 1.0.0,
statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0
- minor enhancements, including:
- add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (#14547)
- include output of failing code style check in message produced by failing easyconfigs style test (#14578)
- bundle LAPACKE with FlexiBLAS 3.0.4 (#14591, #14769)
- add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX (#14634), FactorCopula (#14648), rpact, ldbounds (#14750)
- add extensions to R-bundle-Bioconductor 3.14: ExomeDepth (#14684), DSS (#14748), pathview (#14806)
- various bug fixes, including:
- fix homepage and source_urls for GLIMMER 3.02b (#7945)
- fix source URL for Trilinos 12.12.1 with foss/2019b (#14547)
- use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (#14565)
- fix checksum and versions of annovar v20191024 (#14579)
- add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (#14584)
- retain version in filename for cromwell sources (#14586)
- specify compiler to use in WildMagic easyconfig (#14594)
- avoid need for git build dependency for recent x265 easyconfigs (#14605)
- fix broken patch file for recent GPAW versions (#14619)
- add alternative checksum for Siesta-4.1-MaX-1.0 (#14643)
- add missing PCRE dependency for pullseq + add sanity check commands (#14650)
- use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs (#14655)
- fix name for (binary) AutoDock-Vina v1.1.2 (#14675)
- add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (#14726)
- set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with:
- TensorFlow 2.2.3-2.4.1 with 2020* toolchain (#14729) and 2.5.0+ (#14728)
- Ray-project (#14730)
- enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (#14741)
- add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (#14743)
- also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (#14745)
- do not use external libgcrypt or python for libxslt with recent toolchains (#14756)
- add patches to fix CVE-2021-23437 for Pillow (#14765) and Pillow-SIMD (#14792)
- add libXfont2 patch to fix build when libbsd is present (#14821)
- other changes:
- update Java 1.8 wrapper to 1.8.0_311 for x86_64 (#14644)
- bring gffread back down to GCCcore level for toolchain version 10.3.0 (#14660)
- update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14731, #14755)
- bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738)
v4.5.1 (December 13th 2021)
---------------------------
update/bugfix release
- added example easyconfig files for 71 new software packages:
- ANIcalculator (#14478, #14494, #14510), arrow-R (#14267), ASAP (#14367), BabelStream (#14503), bamtofastq (#14391),
bcbio-gff (#14322), biom-format (#13205), Blosc2 (#14247), boto3 (#14452), Brotli-python (#14528), Brunsli (#14247),
Clang-AOMP (#14327), CLEASE (#14413), CMSeq (#14326), cpu_features (#14385), cromwell (#12125),
cxxopts (#14487, #14504), dRep (#14479), DUBStepR (#14495), eht-imaging (#14239), einops (#14373),
ELFIO (#14488, #14504), elprep (#14422), epiScanpy (#14447), FMM3D (#14257), FORD (#13653), GPy (#14380),
HIP (#14339), idemux (#14499), imagecodecs (#14247), InChI (#13902), jupyter-matlab-proxy (#14270), jxrlib (#14247),
LBFGS++ (#14230), LERC (#14247), libaec (#14247), libavif (#14246), LibLZF (#14246), libnsl (#14494),
libtree (#14501), LPeg (#14157), Megalodon (#14256), nnU-Net (#14249), PAL2NAL (#14430), photontorch (#14410),
pkgconf (#14426), pmx (#14319), PPanGGOLiN (#14449), ProFit (#14340), pugixml (#14367, #14492), PySide2 (#13460),
Relate (#14443), ROCm (#14355), rocm-cmake (#14327), ROCm-CompilerSupport (#14327), rocminfo (#14327),
rocm-smi (#14354), ROCR-Runtime (#14327), ROCT-Thunk-Interface (#14327), SCENIC (#14260), Shasta (#14385),
SimNIBS (#14257), SMV (#14157), SRST2 (#14253), STACEY (#14293), termcolor (#14489, #14504), ThemisPy (#14231),
TOBIAS (#14452, #14458), zfp (#14246), zlib-ng (#14246), Zopfli (#14246)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.6.2, ABRicate 1.0.0, AlphaFold 2.1.1, antiSMASH 6.0.1, Arrow 6.0.0, astropy 4.3.1, BCFtools 1.14,
BeautifulSoup 4.9.3, Boost 1.77.0, bpp 4.4.0, Bracken 2.6.2, CapnProto 0.9.1, CellRanger 6.1.2, Eigen 3.4.0,
enaBrowserTool 1.6, ESMF 8.2.0, Flye 2.9, FMRIprep 1.4.1, FSL 6.0.4, GATK 4.2.3.0, gc 8.2.0, GDB 11.1, git 2.33.1,
Go 1.17.3, Gurobi 9.5.0, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, Infernal 1.1.4, Inspector 2021.4.0 ITK 5.2.1,
jax 0.2.24, Julia 1.7.0, Kent_tools 422, king 2.2.7, libdwarf 20210528, MAFFT 7.490, makeinfo 6.8, Mash 2.3,
matplotlib 3.4.3, MCR R2021b, minimap2 2.22, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, nlohmann_json 3.10.4, NVHPC 21.9,
OpenMPI 4.0.7 + 4.1.2, panaroo 1.2.9, pangolin 3.1.16, pkgconfig 1.5.5, plotly.py 5.4.0, pyfaidx 0.6.3.1,
Pysam 0.17.0, PyTorch 1.10.0, R 4.1.2, R-bundle-Bioconductor 3.14, ReFrame 3.9.1, rpy2 3.4.5, scikit-image 0.18.3,
scikit-learn 1.0.1 SimpleITK 2.1.0, snakemake 6.10.0, SPAdes 3.15.3, tbb 2021.4.0, torchtext 0.10.0,
torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, WPS 4.3.1,
xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4
- minor enhancements, including:
- add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 (#14259)
- add extensions for R v4.1.x:
- geex + momentfit (#14299); StatMatch, leaflet, tmap + collapse (#14328), genoPlotR + penfa (#14433), adcovsim (#14484)
- add M3Drop extension to R-bundle-Bioconductor 3.14 (#14436)
- various bug fixes, including:
- specify to use Python provided as dependency, remove separate_build_dir, and fix URL in comment for Arrow 0.17.1 (#14263)
- fix gettid nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 0.29.1, and 1.1.0 (#14269)
- restore and fix sanity check commands in RStudio-Server 1.4 (#14275)
- add pkg-config build dependency to Python easyconfigs, to ensure OpenSSL wrapper is detected (#14316)
- add patch for UCX v1.11.2 to fix missing include statement for string.h (#14317)
- set $DALTON_TMPDIR to build directory to run Dalton tests (#14341)
- add patch for libfabric v1.12.1 to fix 'unknown link width 0x10' warning (#14387)
- add missing Automake dependency to PhyML 3.3.20200621 (#14397)
- add git as build dependency to Python 3.8.x and 3.9.x easyconfigs (required for pbr extension) (#14421)
- add missing XZ dependency to recent PROJ easyconfigs (#14429)
- fix homepage/source URL for king v2.2.4 (#14444)
- add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers (#14453)
- add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers (#14454)
- add patch to fix CVE-2021-43527 in NSS (#14497)
- pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 (#14502)
- add patch to fix broken (hanging) Mash binaries (#14511)
- add missing Perl build dependency for Longshot (#14535)
- add googletest build dependency for Highway (#14536)
- seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs (#14537)
- other changes:
- rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme (#14262)
- comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (#14335)
- don't add bin subdir to $PATH via modextrapaths in ReFrame easyconfigs (#14415)
- consistently use 'Grace' software name + sync homepage/source_urls (#14493)
- move cxxopts, termcolor and ELFIO header only libraries to SYSTEM toolchain (#14504)
v4.5.0 (October 29th 2021)
--------------------------
feature release
- added easyconfigs for foss/2021b (#14217) and intel/2021b (#14218) common toolchains
- see also https://docs.easybuild.io/en/latest/Common-toolchains.html
- add easyconfig for gobff/2021a toolchain (#14019, #14038)
- added example easyconfig files for 39 new software packages:
- abTEM (#13974), ARTS (#9651), AutoGeneS (#13903), bashplotlib (#13942), CIRI-long (#13985), DFT-D4 (#12803),
ELSI-RCI (#14147), ESL-Bundle (#14179), expecttest (#14106), fdict (#14161), flook (#14161), FreeTDS (#13952),
HDBSCAN (#14062), imkl-FFTW (#14195), isoCirc (#13982), libfdf (#14173), libmbd (#14129), libpspio (#14173),
libSBML (#14050), longread_umi (#13987), Mesa-demos (#14123), MixMHC2pred (#14041), NTPoly (#14183),
OpenSceneGraph (#14197), panaroo (#14203), PEPT (#14077), pycoQC (#14012), python-docx (#13930), QD (#14122),
radeontop (#14124), Rgurobi (#14188), RInChI (#14049), scGeneFit (#13963), swifter (#14114), TOML-Fortran (#13929),
TRUST4 (#14035), ucx-py (#14051), vawk (#14040), VMTK (#14023)
- added additional easyconfigs for various supported software packages, including:
- AlphaFold 2.0.1, artic-ncov2019 2021.06.24, BerkeleyGW 3.0.1, bokeh 2.4.1, Boost.Python 1.76.0, canu 2.2,
Cartopy 0.20.0, CP2K 8.2, CUDA 11.4.2, Dalton 2020.0, dask 2021.9.1, edlib 1.3.9, ELSI 2.7.1, FFTW 3.3.10,
GD 2.73, GDAL 3.3.2, GTDB-Tk 1.7.0, ImageJ 1.52q, jax 0.2.20, Kraken2 2.1.2, leidenalg 0.8.7, libfabric 1.13.2,
libspatialindex 1.9.3, libxc 5.1.6, libxsmm 1.16.2, lifelines 0.26.3, Longshot 0.4.3, LSD2 2.2, MAFFT 7.487,
MEME 5.4.1, MotionCor2 1.4.4, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.3, Nextflow 21.08.0, OpenBLAS 0.3.18,
OpenCV 4.5.3, OrthoFinder 2.5.4, OSU-Micro-Benchmarks 5.8, PhyML 3.3.20200621, PostgreSQL 13.4, pygraphviz 1.7,
pyproj 3.1.0, python-Levenshtein 0.12.1, PyTorch-Geometric 2.0.1, QIIME2 2021.8.eb, Qiskit 0.31.0,
QuantumESPRESSO 6.8, Racon 1.4.21, rampart 1.2.0, rclone 1.56.0, RDKit 2021.03.4, SAMtools 1.13, scanpy 1.8.1,
scikit-allel 1.3.3, SciPy-bundle 2021.10, Seaborn 0.11.2, SHAPEIT4 4.2.2, spglib 1.16.2, UCX 1.11.2,
UCX-CUDA 1.11.2, VSEARCH 2.18.0, Z3 4.8.12, zarr 2.10.1
- minor enhancements, including:
- add JASPAR2020 to R-bundle-Bioconductor 3.13 (#13962)
- add Autotools as build dependency for CubeGUI-4.6 (#14109)
- add compiler/parallel/tcltk R libraries included in base installation to extensions in recent R easyconfigs (#14189, #14190, #14194)
- required for parallel installation of extensions for these R easyconfigs
- also add location to MPI startup tests to $PATH in OSU-Micro-Benchmarks easyconfigs (#14126)
- various bug fixes, including:
- add missing Brotli dependency to freetype (#13915, #14002)
- add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (#13923)
- fix source URL + add alternate checksum for ADMIXTURE 1.3.0 (#13933)
- just use cp to copy stereo_chemical_props.txt to AlphaFold installation directory (#13938)
- add UnZip build dependency to TensorFlow 2.4.1 (#13958), 2.5.0 (#13959) and 2.6.0 easyconfigs (#13960)
- add missing Python dependency for WIEN2k 21.1 + patch to fix build failure for lapw0_mpi with libxc (#13961)
- add additional valid checksum for lhs 1.1.1 extension in recent R 4.0.x and 4.1.0 easyconfigs (#13969)
- fix Fortran system call stdout/err redirection for WIEN2k v21.1 (#13972)
- add OpenSSL dependency to Kent_tools 418 easyconfig to fix a link error (#13989)
- make binutils a build-only dependency for Brotli + add sanity check command (#14004)
- fix installation of Racon v1.4.7 with gcccuda/2019b after move of ClaraGenomicsAnalysis repository (#14010)
- fix source URL for KEGG.db extension in R-bundle-Bioconductor 3.13 easyconfig (since it's a deprecated library now) (#14013)
- add patch for BLIS 0.8.1 to fix dgemm FPE signalling on Broadwell (#14018)
- add patch to fix installation of TensorFlow 2.2.3 on POWER (#14025)
- fix AmberTools v20 easyconfig using intel/2020a toolchain (#14028)
- fix download + permissions of binary for USEARCH v11.0.667 (#14036)
- remove h5py 3.x dependency for Keras with 2020b toolchain, since TensorFlow provides (and requires) h5py 2.x (#14052)
- correctly specify install prefix for CUDA in OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a (#14063)
- add patch to fix failing file system cache test for jax on recent Linux kernels (#14067, #14070)
- fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (#14073)
- add missing dependencies for recent LibTIFF versions: XZ, jbigkit, zstd (#14079)
- add missing header file to existing versions of jbigkit (#14081)
- fix source URL for SUNDIALS 5.x (#14092, #14096)
- add Perl and Python runtime dependencies to Bowtie2 2.4.4 (#14097)
- fix source URL for SCOTCH 6.1.0 (#14099)
- drop tcmalloc from SymEngine as it causes crashes with scipy (#14119)
- fix homepage + description in SimpleITK easyconfigs (#14125)
- add missing scripts from utils and analysis_scripts to bin for cryoDRGN (#14137)
- patch rsync_from_ncbi.pl in Kraken2 v2.1.2 to allow syncing with NCBI servers over HTTPS (#14148)
- skip mkl_fused_batch_norm_op_test test (broken on AMD EPYC systems) for TensorFlow 2.5.0 and 2.6.0 (#14151, #14153)