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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 16,138 easyconfig files, for 2,904 different software packages,
incl. 39 different (compiler) toolchains.
4.7.0 (Janurary 9th 2023)
-------------------------
feature release
- added easyconfigs for foss/2022a, intel/2022a 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)
- fix incorrect module load message and update morphology plugin of ImageJ 1.51k (#14152)
- fix XCrySDen v1.6.2 linking to libdl and Togl (#14160)
- add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0 (#14177)
- add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests (#14178)
- fix spatstat.* downloads for Seurat v4.0.1 (#14199)
- add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection (#14212)
- other changes:
- remove help2man build dependency for flex using system toolchain (because it requires Perl) (#13922)
- use proper dependency for python-Levenshtein in CIRI-long easyconfig (#13985)
- in-place updates for foss/2021b and intel/2021b common toolchains
- update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (#14090)
- update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (#14164)
- update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 with GCCcore/11.2.0 toolchain (#14167)
- update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (#14176)
- remove format mapping from homepage of Subread easyconfigs (#14145)
- add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 0.3.4 with GCC/11.2.0 toolchain (#14225)
v4.4.2 (September 7th 2021)
---------------------------
update/bugfix release
- added easyconfig for foss/2021.07 (candidate for foss/2021b) (#13788) and iomkl/2021a (#13521) toolchains
- added example easyconfig files for 79 new software packages:
- AlphaFold (#13867), andi (#13768), aria2 (#13709), AUTO-07p (#13831), babl (#13216), BAli-Phy (#13484),
biogeme (#13735), Bio-SearchIO-hmmer (#13419), BuDDy (#13907), c-ares (#13709), CellRank (#13408), Coin (#13818),
Co-phylog (#13769), cppy (#13823), CREST (#13648), CRISPR-DAV (#13139), CSBLAST (#13794), DGL (#13793),
DistributedStream (#13659), Excel-Writer-XLSX (#13139), FBPIC (#13500), freebayes (#12859), freud-analysis (#13354),
fumi_tools (#13517), GEGL (#13216), GIMP (#13216), glib-networking (#13216), GOATOOLS (#13364, #13629),
gofasta (#13651), GTK2 (#13900), GTK3 (#13900), Highway (#13453), hipSYCL (#13837), ISA-L (#13663), jax (#13760),
JSON-GLib (#13216), Kalign (#13463), LADR (#13351), lDDT (#13794), libdivsufsort (#13768), libjxl (#13453, #13829),
libmypaint (#13216), libtecla (#13908), lie_learn (#13793), longestrunsubsequence (#13800), Maude (#13909),
mimalloc (#13726), MINPACK (#13802), Mish-Cuda (#13759, #13784), muparserx (#13779), nlohmann_json (#13777),
OpenStackClient (#13644), OSPRay (#12852), pandapower (#13687), pangolin (#13733, #13848), PSIPRED (#13794),
PYPOWER (#13689), PyPSA (#13673), PyRosetta (#13793), pysamstats (#13139), pytest-benchmark (#13622),
python-isal (#13663), QCxMS (#13650), RepeatModeler (#13126), Schrodinger (#11698), sklearn-som (#13699),
SoQt (#13818), spdlog (#13778), SpectrA (#13743), SymEngine-python (#13652), SyRI (#13800), torchinfo (#13662),
TRAVIS-Analyzer (#13503), UShER (#13708), Vampire (#13352), VBZ-Compression (#13536), VisPy (#13468),
wgsim (#13475), Yices (#13906)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2020.eb, ANTs 2.3.5, AOCC 3.1.0, Arb 2.19.0, archspec 0.1.2, Armadillo 10.5.3, ASE 3.22.0,
Autotools 20210726, BamTools 2.5.2, bgen 4.1.3, Biopython 1.79, bitarray 1.5.3, Boost 1.76.0, Bowtie2 2.4.4,
bpytop 1.0.67, Cartopy 0.19.0.post1, Centrifuge 1.0.4, Clang 12.0.1, CMake 3.21.1, CRISPResso2 2.2.1, CUDA 11.4.1,
cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, DIAMOND 2.0.11, DROP 1.1.0, Dsuite 20210718, dtcmp 1.1.2, ecCodes 2.22.1,
Elk 7.2.42, ESMF 8.1.1, expat 2.4.1, fastq-tools 0.8.3, Fiona 1.8.20, FLINT 2.7.1, g2clib 1.6.3, g2lib 3.2.0,
GCC(core) 11.2.0, GDCM 3.0.8, GDRCopy 2.3, GenomeTools 1.6.2, GffCompare 0.12.2, gffread 0.12.7, GLib 2.69.1,
GMT 6.2.0, Go 1.16.6, GPAW 21.6.0, Gradle 6.9.1.eb, GROMACS 2021.3, HarfBuzz 2.8.2, HDF5 1.12.1, Horovod 0.22.1,
hwloc 2.5.0, hypothesis 6.14.6, igraph 0.9.4, ImageMagick 7.1.0, IMOD 4.11.5, IPython 7.26.0, Java 16,
Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kent_tools 418, lavaan 0.6-9, libfabric 1.13.0, libffcall 2.4,
libffi 3.4.2, libgeotiff 1.7.0, libRmath 4.1.0, LIBSVM 3.25, LibTIFF 4.3.0, likwid 5.2.0, LLVM 12.0.1, LMDB 0.9.29,
magma 2.6.1, MariaDB 10.6.4, MATIO 1.5.21, matplotlib 3.4.2, MEGA 10.0.5, Mesa 21.1.7, Meson 0.59.1,
Metal 2020-05-05, Mini-XML 3.2, molmod 1.4.8, MPICH 3.4.2, nanopolish 0.13.3, NCCL 2.10.3, ncdu 1.16, NCO 5.0.1,
neptune-client 0.10.5, netcdf4-python 1.5.7, networkx 2.5.1, nodejs 14.17.6, NSPR 4.32, NSS 3.69, NVHPC 21.7,
OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2106, OpenMM 7.5.1, OpenMolcas 21.06, openpyxl 3.0.7,
Pango 1.48.8, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.13, PCRE2 10.37, PCRE 8.45, Perl 5.34.0,
PETSc 3.15.1, petsc4py 3.15.0, Pillow 8.3.1, Pillow-SIMD 8.3.1, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0,
poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, pybind11 2.7.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1,
PyQt5 5.15.4, pyshp 2.1.3, Python 3.9.6, python-igraph 0.9.6, QTLtools 1.3.1, RAxML-NG 1.0.3,
R-bundle-Bioconductor 3.13, re2c 2.2, ReFrame 3.8.0., RStudio-Server 1.4.1717, Rust 1.54.0, Scalasca 2.6,
scVelo 0.2.3, Shapely 1.8a1, shrinkwrap 1.1.0, SLEPc 3.15.1, slepc4py 3.15.1, snakemake 6.6.1, snappy 1.1.9,
snippy 4.6.0, snpEff 5.0e, SOCI 4.0.2, SpaceRanger 1.3.0, Spack 0.16.2, spatialreg 1.1-8,
spglib-python 1.16.1, SQLite 3.36, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, SymEngine 0.7.0,
TensorFlow 2.6.0, TetGen 1.6.0, Tkinter 3.9.6, torchtext 0.9.1, tqdm 4.61.2, UCX 1.11.0, UCX-CUDA 1.11.0,
unrar 6.0.2, util-linux 2.37, VTune 2021.6.0, WIEN2k 21.1, WPS 4.2, WRF 4.3, X11 20210802,
x264 20210613, xarray 0.19.0, XlsxWriter 1.4.4, XML-Parser 2.46, zstd 1.5.0
- minor enhancements, including:
- add extensions to recent R v4.x easyconfigs: PCAmatchR (#13448), hal9001 (#13451), cobalt (#13544), CBPS (#13549),
SBdecomp (#13565), lwgeom (#13674), naturalsort (#13762), finalfit + gtsummary (#13766)
- add VBZ compress capability to nanopolish 0.13.3 (for fast5 files) (#13536)
- add CMake build dependency to easyconfig for tbb 2020.03 (#13704)
- also build shared libs for MUMPS 5.3.5 (#13702) and 5.4.0 (#13705)
- add dependency on pkg-config to OpenSSL wrappers (#13765)
- various bug fixes, including:
- fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost (#11577)
- fix sanity check error for OpenCV v4.5.1 by adding (and using) freetype and HarfBuzz dependencies (#12517)
- add patches for TensorFlow 1.13.1 to fix installation (#13326)
- remove Python 2.6 from list of supported Python versions in setup.py (#13349)
- switch back to Bundle easyblock for PyQt5 5.15.1 + add back source URLs for components (#13371)
- add pkg-config build dependency for GDAL 3.2.1 (#13383, #13808), Rust (#13538), GenomeTools (#13805), x264 (#13834)
- add missing Python 3 build dependency for Rust v1.52.1 (#13399)
- fix order of cffi extension in old Python easyconfigs (#13400)
- patch out __asm__ use in ctffind to avoid build failure on ppc64le (#13409)
- disable building man pages in Gdk-Pixbuf (#13410)
- add missing Bio-Search-hmmer dependency for prokka (#13419)
- avoid downloading old numpy version during install for h5py (#13428)
- add patch for Qt5 5.8.0 to fix compilation failure in webkit (#13434)
- avoid downloading and building freetype and qhull for matplotlib 3.4.2 (#13437)
- fix order of components in recent GTK+ easyconfigs to avoid dependency on system GTK+ in GTK+ themes (#13449)
- fix Python 2.7.13 easyconfigs by adding missing extensions (#13456)
- add TensorFlow patch to fix crash on shutdown (#13462)
- allow for non-x86_64 in postinstallcmds for CuPy (#13501)
- disable default EULA acceptance in easyconfig for NVHPC v21.5 (#13516)
- fix error with p7zip's 7z command not finding 7z.dll (#13542)
- patch MaxBin2 Perl script to use provided Perl dependency (#13551)
- add missing zlib dependency to libarchive (#13579)
- fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig with GCCcore/11.2.0 toolchain) (#13581)
- fix build of DIRAC 19.0 easyconfig with high compiler optimizations (#13613)
- fix source URLs and add alternative checksum for Hypre 2.15.1 (since it moved to a different GitHub repo) (#13616)
- add new source URL for Mesa easyconfigs using 2017b toolchain (#13617)
- avoid MPICXX dependency in SimpleElastics ITK (#13623)
- add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (#13628)
- add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault) (#13665)
- enable EGL in recent libepoxy ECs (#13684)
- remove unused buildcmd from libgpuarray easyconfigs (#13720)
- add patch to fix building Qt5.10.1 against newer glibc (#13730)
- add Python 3 as a builddependency to recent fontconfig easyconfigs (#13731)
- update source_URL in BLAST 2.2.26 easyconfig (#13732)
- restore error message on failing easyconfigs test suite, required by bot to determine end of output of test suite (#13745, #13770)
- add Perl build dependency to recent Clang easyconfigs (#13746)
- disable using system Valgrind in the json-c tests (#13750)
- use Archive source URL for spatstat.geom extension in Seurat (#13761)
- add ld.gold relocts patch to binutils 2.30 (#13785)
- add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 (#13786)
- add alternative checksum for AFNI 18.3.00 (#13790)
- update tensorflow-probability easyconfigs to include '--release' flag in installopts (#13810)
- fix source URL for DB 18.1.32 (#13813)
- add missing cppy build dependency for matplotlib 3.4.2 (#13823)
- disable bash completion in recent x264 easyconfigs (#13834)
- add Perl as build dependency for ELPA 2021.05.001 + patch to fix hardcoded /usr/bin/perl (#13835)
- add archive source URL to Spark 3.x easyconfigs to fix broken download (#13842)
- fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 (#13861)
- add Perl build dependency for HMMER 3.3.2 + patch to ensure it is used (#13870)
- stick to intel-compilers toolchain for DFT-D3 v3.2.0 (#13878)
- add missing flex build dependency for leidenalg (#13884)
- update CMake build dependency for Eigen 3.3.4 + 3.3.5 (#13889)
- fix source URL for Yasm 1.3.0 (+ add missing checksum) (#13901)
- update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check (#13910)
- fix shebang for RepeatMasker 4.1.2-p1 Perl script (#13911)
- other changes:
- use custom ORCA easyblock in easyconfigs for ORCA v4.x (#13348)
- move archived easyconfig files to correct __archive__ folder (#13422)
- rename NINJA to TWL-NINJA to avoid nameclash (#13529)
- remove superflous configopts and add sanity checks/checksums in CLHEP easyconfigs (#13614)
- remove superflous -DCMAKE_BUILD_TYPE configuration option in Arrow easyconfigs (#13615)
- switch ITK easyconfigs to CMakePythonPackage easyblock, also enable -DITK_USE_SYSTEM_HDF5 configuration option, fix download URLs (#13619)
- use build_type instead of -DCMAKE_BUILD_TYPE=RELEASE in configopts in MMseqs2 easyconfigs (#13620)
- avoid using system GTK+3 and remove -DCMAKE_BUILD_TYPE=RELEASE configure option in OpenCV easyconfigs (#13621)
- remove -DCMAKE_BUILD_TYPE=RELEASE configure option and add checksums in LLVM easyconfigs (#13624)
- create libtinfo symlinks in easyconfigs for ncurses with system toolchain (#13658), 6.1 (#13661) and 6.2 (#13660)
- increase test timeouts for PyTorch 1.8.1 and 1.9.0 (#13700)
- rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda, to ensure that get_software_root('CUDA') used in easyblocks works (#13874)
- use CUDA instead of CUDAcore in recent NVHPC comments (#13875)
v4.4.1 (July 6th 2021)
----------------------
update/bugfix release
- added example easyconfig files for 39 new software packages:
- AMPHORA2 (#13003), AOMP (#12909), CAMPARI (#13152), CSB (#12877), dijitso (#10719), DosageConvertor (#13278),
dSFMT (#12971), exiv2 (#13204), FEniCS (#10719), FreeFEM (#9902), futhark (#12921), futile (#12864),
gappa (#13186), GenomeWorks (#13083, #13092), gexiv2 (#13204), HAL (#13267), hipify-clang (#12961), inline (#12029),
libcint (#13214), LTR_retriever (#13125), mapDamage (#13172), MbedTLS (#13061), microctools (#13010),
Nektar++ (#12664), NINJA (#13125), OBITools3 (#12969), ont-fast5-api (#13033), OpenMM-PLUMED (#13268),
phototonic (#13241), PyFoam (#12675), RagTag (#13247), RcppGSL (#13172), RECON (#13123), RepeatScout (#13124),
retworkx (#13228), UCX-CUDA (#13260), unimap (#13247), Vala (#13204), WhatsHap (#12989)
- added additional easyconfigs for various supported software packages, including:
- Amber 20.11, BBMap 38.90, Beast 2.6.4, BLIS 3.0 (AMDo fork), Bonito 0.4.0, CellRanger-ARC 2.0.0,
CellRanger-ATAC 2.0.0, Check 0.15.2, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, cuDNN 8.2.1.32, CVXOPT 1.2.6,
DOLFIN 2019.1.0.post0, eggnog-mapper 2.1.4, ELPA 2021.05.001, FDS 6.7.6, FFC 2019.1.0.post0, FFmpeg 4.3.2,
FIAT 2019.1.0, flatbuffers 2.0.0, flatbuffers-python 2.0, FLTK 1.3.6, gc 8.0.4, GCC 8.4.0 + 9.4.0, GDAL 3.3.0,
Gdk-Pixbuf 2.42.6, geopy 2.1.0, Ghostscript 9.54.0, git 2.32.0, GitPython 3.1.18, GLFW 3.3.4, gmsh 4.8.4,
gnuplot 5.4.2, GnuTLS 3.7.2, Go 1.16.5, GObject-Introspection 1.68.0, gperftools 2.9.1, GraphicsMagick 1.3.36,
Graphviz 2.47.2, GSL 2.7, GTK+ 2.24.33, Guile 2.2.7, h5py 3.2.1, HarfBuzz 2.8.1, Horovod 0.22.0, Hypre 2.21.0,
ICU 69.1, ImageMagick 7.0.11-14, IOR 3.3.0, IPython 7.25.0, IRkernel 1.2, ispc 1.16.0, JupyterLab 3.0.16,
LDC 1.26.0, libcerf 1.17, libepoxy 1.5.8, libgd 2.3.1, libStatGen 1.0.15, libxc 5.1.5, LittleCMS 2.12,
LMfit 1.0.2, Lua 5.4.3, M4 1.4.19, MCR R2021a.3, medaka 1.4.3, Mercurial 5.8, minimap2 2.20, MMseqs2 13,
MrBayes 3.2.7, MUMPS 5.4.0, NCCL 2.9.9, netCDF 4.8.0, Nim 1.4.8, nodejs 14.17.0, Nsight-Compute 2021.2.0,
numba 0.53.1, NVHPC 21.5.eb, nvtop 1.2.1, Octave 6.2.0, OPARI2 2.0.6, openkim-models 20210128, OpenMPI 4.0.6,
OTF2 2.3, p11-kit 0.24.0, Pango 1.48.5, parallel 20210622, petsc4py 3.12.0, picard 2.25.5, Pillow 8.2.0,
PROJ 8.0.1, protobuf 3.17.3, protobuf-python 3.17.3, PSolver 1.8.3, PySCF 1.7.6, pyspoa 0.0.8, pytest-xdist 2.3.0,
PyTorch 1.9.0, PyYAML 5.4.1, Qhull 2020.2, Quandl 3.6.1, R 4.0.5 + R 4.1.0, Ragout 2.3, RE2 2021-06-01,
ReFrame 3.6.2, RepeatMasker 4.1.2, rgdal 1.5-23, RMBlast 2.11.0, Ruby 3.0.1, scikit-learn 0.24.2,
Score-P 7.0, Seurat 4.0.3, slepc4py 3.12.0, spoa 4.0.7, Subread 2.0.2, Subversion 1.14.1, SuiteSparse 5.10.1,
sympy 1.8, tensorboardX 2.2, TensorFlow 2.5.0, Tk 8.6.11, tmux 3.2a, torchtext 0.8.1, torchvision 0.9.1,
UDUNITS 2.2.28, UFL 2019.1.0, utf8proc 2.6.1, VEP 103.1, VMD 1.9.4a51, vsc-mympirun 5.2.6, XCFun 2.1.1,
Xvfb 1.20.11, Z3 4.8.11, ZeroMQ 4.3.4
- minor enhancements, including:
- update cuDNN 8.0.x easyconfigs with a download location (#12368)
- add extensions to recent R easyconfigs: GxEScanR (#13039), cSEM (#13208), cubelyr + broom.mixed (#13252),
grf (#13261), twang + xgboost (#13284), neuralnet (#13330)
- add check to easyconfigs test suite to ensure OpenSSL wrapper is used in easyconfigs using a recent toolchain (#13079)
- add gipaw to QuantumESPRESSO/6.7 (#13087)
- add checksum for aarch64 installation file for CUDAcore easyconfigs (#13014, #13097)
- add Perl dependency to makeinfo easyconfigs (#13166)
- set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper (#13188)
- add JIT support for CUDA 11 to PyTorch 1.7.1 (#13207)
- add 'ninja --version' as sanity check command in Ninja easyconfigs (#13222)
- code cleanup + improvements for easyconfigs test suite (#13257)
- various bug fixes, including:
- download sources via git for XGBoost 20171120 easyconfig due to use of submodules (#6880)
- add elfutils as build dependency for Clang 8.0.x and 9.0.1 (#13015) and Clang 11.0.1 (#13008) easyconfigs that have a CUDA dependency
- add missing CMake option to Geant4 v10.7.1 in order to actually use external CLHEP (#13019)
- add new checksum for mvabund extension to R v4.0.4 eaysconfigs (#13020, #13021)
- add patch to fix numpy test_ccompiler_opt in SciPy-bundle v2021.05 (#13042)
- add patch to fix installation of HDF 4.2.15 on aarch64 (#13059)
- make sure that MbedTLS' Makefile uses 'python' rather than 'python2' (#13061)
- fix checksum for snpEff 5.0 (#13062)
- fix source URL for LIBSVM 3.24 by downloading from GitHub (#13076)
- add preinstallopts for minimap2 to fix installation on aarch64 (#13080)
- add patch for GCC 10.2.0 to fix internal compiler error on aarch64 (#13086)
- switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b (#13103)
- add astor to dependencies of TensorFlow with 2019b (#13111) and 2020b (#13103, #13112) toolchains
- break cyclic dependency between groff, makeinfo and Perl by adding Perl-minimal and makeinfo-minimal easyconfigs (#13163-#13165)
- add missing rgdal dep to R-INLA (#13179)
- add patch to fix uniq operation in TensorFlow 2.4.1 (#13181)
- add Perl build dependency for PnetCDF 1.12.1 (#13183)
- disable own avx detection of libfabric v1.12.1 (#13215)
- add GCCcore-[1-9][0-9].x to test_dep_versions_per_toolchain_generation (#13243, #13249, #13251)
- add patch to fix installation of TensorFlow 2.0.x (#13248)
- add patch for recent GCCcore versions to fix compability with CUDA 11 (#13290)
- fix install step for glew (#13297)
- update Boost 1.74.0 easyconfigs to use tagged_layout rather than boost_multi_thread (#13300)
- avoid using PMIx from system instead of PMIx dependency specified via --with-pmix for OpenMPI 4.x (#13307)
- add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc (#13310)
- add patch for OpenMPI 4.0.x to fix building against (system) UCX version > 1.7 (#13329)
- fix build of manta 1.6.0 on top of Boost 1.74.0 (#13338)
- fix recent taxator-tk easyconfigs by adding (back) -DBoost_NO_BOOST_CMAKE=ON configure option (#13342)
- other changes:
- disable debuginfod for elfutils to minimize required dependencies (#13034)
- add bare Python 3.9.5 easyconfig and use that as builddep for LLVM 11.1.0 (#13035)
- remove misleading comment from Python >= 3.7 easyconfigs, libffi is now also required for Python itself (no longer bundled) (#13041)
- use new custom easyblock in torchvision easyconfigs (#13102)
- remove superflous TensorFlow patch (#13223)
- cleanup of easyconfigs for (bundles) of Python packages: remove default PYPI_SOURCE source URLs + use PythonBundle rather than Bundle easyblock (#13253, #13295, #13336)
- update README with instructions for MATLAB easyconfigs (#12597)
v4.4.0 (June 2nd 2021)
----------------------
feature release
- added easyconfigs for new Fujitsu toolchain: FCC/4.5.0 (#12999, #12995, #13007), ffmpi/4.5.0 (#13000) and Fujitsu/21.05 (#13001, #13007)
- add easyconfigs for updates of common toolchains: foss/2021a (#12867, #12975), intel/2021a (#12885, #12975)
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added easyconfig for gomkl/2021a toolchain (#12987)
- added example easyconfig files for 58 new software packages:
- Archive-Zip (#12651), BirdNET (#12737, #12712, #12737), cell2location (#12448), cryoDRGN (#12704),
dm-reverb (#12824), DROP (#12559, #12801, #12950), fastahack (#12841), fermi-lite (#12856), filevercmp (#12841),
FlexiBLAS (#12476), freetype-py (#12918), fsom (#12841), garnett (#12529), gawk (#12716), gemmi (#12855),
georges (#12570), hifiasm (#12897), intervaltree (#12838), LDC (#12671), libidn2 (#12670), librosa (#10477),
librsb (#12780), line_profiler (#12556), loompy (#12804), mmtf-cpp (#12580), mongolite (#12632), msgpack-c (#12580),
multichoose (#12839), networkTools (#12810), NewHybrids (#12528), Octopus-vcf (#12598), onedrive (#12671),
p4-phylogenetics (#12549), pagmo (#12678), pyfaidx (#12872), pyfasta (#12952), pygmo (#12678), pysheds (#12791),
R-INLA (#12955, #12927, #12955), RegTools (#12874), request (#12448), rMATS-turbo (#12982), scanpy (#12731),
SeqLib (#12856), SeuratData (#12993), SeuratWrappers (#12994), smithwaterman (#12841), snp-sites (#12900),
SSW (#12856), tabixpp (#12837), TagDust (#11599), TALON (#12963), tMAE (#12559), TranscriptClean (#12952),
umap-learn (#12448), vcflib (#12841), xESMF (#12799), XlsxWriter (#12820)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.4.1, apex 20210420, astropy 4.2.1, binutils 2.36.1, BLIS 0.8.1, Bonito 0.3.8, BUSCO 5.1.2, canu 2.1.1,
carputils 20210513, CastXML 0.4.3, ccache 4.2.1, CDO 1.9.10, CIRCexplorer2 2.3.8, CLHEP 2.4.4.0, CMake 3.20.1,
CNVkit 0.9.8, CUDA(core) 11.3.0, CuPy 8.5.0, cURL 7.76.0, DFA 2.1.2, Doxygen 1.9.1, Eigen 3.3.9, FastANI 1.33,
FFTW 3.3.9, GATK 4.2.0.0, GCC 10.3.0 + 11.1.0, GDB 10.2, gdc-client 1.6.0, GDRCopy 2.2, Geant4 10.7.1,
Geant4-data 20210510, GeneMark-ET 4.65, glew 2.2.0, GLib 2.68.2, GLPK 5.0, GMP 6.2.1, Go 1.16.3, Graphviz 2.47.0,
GROMACS 2021.2, GStreamer 1.18.4, GTDB-Tk 1.5.0, Gurobi 9.1.2, HMMER 3.3.2, Horovod 0.21.3, hwloc 2.4.1,
hypothesis 6.13.1, IGV 2.9.4, impi 2021.2.0, imkl 2021.2.0, intel-compilers 2021.2.0, JasPer 2.0.28, Julia 1.6.1,
Kraken2 2.1.1, KronaTools 2.8, libarchive 3.5.1, libdeflate 1.7, libdrm 2.4.106, libfabric 1.12.1, libreadline 8.1,
libRmath 4.0.0, libsndfile 1.0.31, LIBSVM 3.24, LibTIFF 4.2.0, libunwind 1.5.0, libwebp 1.2.0, LLVM 11.1.0,
LMDB 0.9.28, LUMPY 0.3.1, lz4 1.9.3, Mako 1.1.4, MATLAB 2021a, Mesa 21.1.1, meshalyzer 2.2, Meson 0.58.0,
MetaBAT 2.15, metaWRAP 1.3, minimap2 2.18, Molden 6.8, MotionCor2 1.4.2, ncview 2.1.8, NetPIPE 5.1.4, nettle 3.7.2,
NiBabel 3.2.1, Nilearn 0.7.1, Nim 1.4.6, Ninja 1.10.2, NLopt 2.7.0, NSS 3.65, numactl 2.0.14, NWChem 7.0.2,
OpenBLAS 0.3.15, openCARP 6.0, OpenEXR 3.0.1, OpenMM 7.5.0, OpenMPI 4.1.1, OpenSSL 1.1 (wrapper),
OSU-Micro-Benchmarks 5.7.1, Pandoc 2.13, parallel 20210322, parasail 2.4.3, PAUP 4.0a168, PCRE2 10.36, Perl 5.32.1,
pigz 2.6, PMIx 3.2.3, Primer3 2.5.0, PRSice 2.3.3, py-aiger 6.1.14, pybind11 2.6.2, PyCharm 2021.1.1, pydot 1.4.2,
pyproj 3.0.1, PySAT 0.1.7.dev1, PyTorch 1.8.1, python-parasail 1.2.4, Pylint 2.7.4, Python 3.9.5, Qt5 5.15.2,
R-keras 2.4.0, rasterio 1.2.3, RAxML-NG 1.0.2, rclone 1.54.1, re2c 2.1.1, ReFrame 3.5.2, Rmath 4.0.4, Rust 1.52.1,
Sambamba 0.8.0, samblaster 0.1.26, samclip 0.4.0, scikit-allel 1.3.2, SciPy-bundle 2021.05, SCons 4.1.0.post1,
snakemake 6.1.0, SQLite 3.35.4, SRPRISM 3.1.2, Tcl 8.6.11, TCLAP 1.2.4, tmux 3.2, tqdm 4.60.0, UCX 1.10.0,
Valgrind 3.17.0, WannierTools 2.5.1, wget 1.21.1, wxWidgets 3.1.4, X11 20210518, x264 20210414, x265 3.5,
xorg-macros 1.19.3, YAXT 0.9.0, zarr 2.8.1, zstd 1.4.9
- minor enhancements, including:
- add additional extensions to R v4.0.3 and v4.0.4: miceadds, visdat, UpSetR, naniar, stringdist,
image.binarization (#12735), lassosum (#12821), lslx, regsem, semPLS (#13005)
- add GenABEL to R-bundle-Bioconductor (#12822)
- various bug fixes, including:
- disable automatic acceptance of NVHPC EULA (#12014)
- enhance RStudio-Server, add patch to inherit environment variables, add sanity check commands to verify installation (#12544)
- add fix to scipy to handle NaN arguments to "vi" function (#12551)
- copy all binaries + examples & co for PAML v4.9j (#12567)
- add patch to fix hardcoded num_cores in DMCfun extension included with R 4.0.x (#12583)
- backport Charm++ patch for NAMD/2.14 on intel/2020a to handle newer glibc (#12594)
- add setuptools_scm and pytest-runner extensions to Pylint easyconfigs (#12599)
- fix typo in Delly easyconfig to actually do parallel build (#12633)
- fix potential memory leak in OpenBLAS 0.3.12 (#12649)
- consistently use pip to install Python packages in recent Python easyconfigs (#12650)
- replace bintray source url for Groovy (#12652)
- add missing Python & Perl dependencies to for AUGUSTUS v3.4.0 with foss/2020b (#12662)
- fix wget dependency: use libidn2 rather than libidn (#12670)
- fix source URLs for recent ELPA versions (#12700)
- override host compiler check in CUDAcore (#12701)
- add Python build dependency to libpsl 0.21.0 easyconfigs (#12715)
- fix error in libgpg-error 1.36 with gawk builtin (#12716)
- add libtool build dependency to leidenalg (#12741)
- fix source URLs for Boost 1.71.0 - 1.74.0 easyconfigs (#12743) and Boost.Python (#12744)
- add patches for PyTorch 1.7.1 avoiding failures on POWER and A100 (#12753)
- add patch for OpenPGM 5.2.122 eaysconfigs to fix non-existent directory in *.pc (pkgconfig) file (#12774)
- add missing Perl build dependency to recent wget easyconfigs (#12787)
- make sure Python dependency is used in preCICE 2.x easyconfigs (#12793)
- don't skip source step in FastTree easyconfigs + fix SHA256 checksum for FastTree 2.1.11 (#12794)
- add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64 (#12836)
- add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 (#12865)
- fix checksum for MaxBin 2.2.7 (#12869)
- run 'make clean' before building FragGeneScan, to clean up object files included in source tarball (#12870)
- clean up install of KronaTools (#12871)