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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 15,020 easyconfig files, for 2,736 different software packages,
incl. 37 different (compiler) toolchains.
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)
- add UCX dependency to OneAPI versions of impi (#12873)
- correct description in libdeflate easyconfig (#12886)
- override Makefile with hardcoded CC=cc in UnZip easyconfigs (#12887)
- fix compatibility of FLAIR v1.5.1-20200630 with rpy2 v3.x (#12899)
- fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking (#12912)
- fix source URLs in BLAST 2.10.x easyconfigs (#12914)
- add missing xproto build dependency to imake easyconfig (#12930)
- add patch to fix GCC 10.2.0 rejecting valid code on PPC (#12948)
- in easyconfig tests, check version of dependencies named Python, not if dependencies with certain versions are named Python (#12962)
- update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes (#12967, #12988)
- fix download URL for DB 18.1.40 (#12974)
- fix test failure in TensorFlow 2.4.1 on recent CUDA drivers (#12979)
- fix error in configopts for netCDF and HDF5 and add missing dependencies of ABINIT 9.x (#12981)
- add patch to fix buffer overflow in OpenMPI 4.1.x (#12983)
- other changes:
- update setup.py to indicate compatibility with Python 3.8 and 3.9 (#12565)
- add -Java versionsuffix for Hadoop easyconfig using GCCcore/10.2.0 toolchain, since it depends on Java 1.8 (#12709)
- remove unneccessary workaround for missing version of OpenDataCube and Spyder for 2020+ toolchains (#12757)
- remove 'unpack_sources = False' from recent easyconfigs that use a *.whl file as source (#12783)
- whitelist Seaborn 0.10.1 for NanoComp 1.13.1 and NanoPlot 1.33.0 (#12790)
- add check to make sure that source step is not being skipped (#12807)
- use EasyConfig.disable_templating method in test suite (#12848)
- disable usNIC by default in libfabric to avoid problems due to linking to both libnl and libnl-3 (#12854)
- use OpenSSL wrapper as dependency in easyconfigs using GCCcore/10.3.0 toolchain (#12922, #12944)
- dump easyconfig before initializing easyblock in order to compare it with original easyconfig (#12925)
- remove postinstallcmds from imkl 2020.x easyconfigs, easyblock now installs examples (#12937)
v4.3.4 (April 9th 2021)
-----------------------
update/bugfix release
- added easyconfig for goblf/2020b toolchain (#12381, #12535)
- added example easyconfig files for 41 new software packages:
- amplimap (#12205), BEEF (#12104), bpp (#12036), Brotli (#11651), CDAT (#12322), cicero (#12252),
CIF2Cell (#12258), CompareM (#9377), DL_POLY_4 (#12324), DMCfun (#12412), ESMPy (#12339), FLAC (#12300),
gdbm (#12322), GPyOpt (#12524), json-c (#12344), libcdms (#12322), libdrs (#12322), libogg (#12285),
libvorbis (#12300), LncLOOM (#12287), LPJmL (#12344), maze (#12354), MetaEuk (#12188), mrcfile (#12497),
Myokit (#12261), NCCL-tests (#12415), pyABC (#12329), PyCifRW (#12258), PyOD (#12507), pyro-api (#12447),
pyro-ppl (#12447), R-opencv (#12226), Ratatosk (#12443), RevBayes (#12419), sansa (#12354), scikit-cuda (#12352),
Seeder (#9057), suave (#12354), voltools (#12497), vorbis-tools (#12300), YACS (#12309)
- added additional easyconfigs for various supported software packages, including:
- AOCC 3.0.0, Arriba 2.1.0, ArviZ 0.11.1, arpack-ng 3.8.0 BCFtools 1.12, BEDTools 2.30.0, BUSCO 5.0.0, BioPerl 1.7.8,
Blosc 1.21.0, Boost.Python 1.74.0, bitarray 1.2.1, bokeh 2.2.3, CP2K 8.1, CUDAcore 11.2.2, CellRanger 6.0.0,
Clang 11.0.1, DIAMOND 2.0.7, Delly 0.8.7, dask 2021.2.0, dm-tree 0.1.5, Elk 7.0.12, Extrae 3.8.0, FLUENT 2021R1,
FabIO 0.11.0, Fiji 20201104, Flye 2.8.3, FreeSurfer 7.1.1, GDAL 3.2.1, GEOS 3.9.1, GLFW 3.3.3,
GMAP-GSNAP 2020-12-17, GROMACS 2021, GetOrganelle 1.7.4, gmsh 4.7.1, HTSeq 0.11.3, HTSlib 1.12, Hypre 2.20.0,
hyperopt 0.2.5, iVar 1.3.1, igraph 0.9.1, Jansson 2.13.1, Kent_tools 411, LAPACK 3.9.1, LAST 1179, LibSoup 2.72.0,
libxc 5.1.3, MAFFT 7.475, MCR R2020a.6 + R2020b.5 + R2021a.0.eb, MDTraj 1.9.5, MUMPS 5.3.5, MaSuRCA 4.0.1,
Mercurial 5.7.1, Monocle3 0.2.3, NGS 2.10.9, NVHPC 21.2, NetLogo 6.2.0, Nextflow 21.03.0, ncbi-vdb 2.10.9,
OSU-Micro-Benchmarks 5.7, OpenCV 4.5.1, OpenEXR 2.5.5, OptiX 7.2.0, PETSc 3.14.4, PLUMED 2.7.0, PROJ 7.2.1,
PyAMG 4.0.0, PyCUDA 2020.1, PyCairo 1.20.0, PyOpenCL 2021.1.2, PyTorch-Geometric 1.6.3, p7zip 17.03, pFUnit 4.2.0,
picard 2.25.1, pocl 1.6, preCICE 2.2.0, protobuf 2.5.0, pymatgen 2022.0.4, python-igraph 0.9.0, Qtconsole 5.0.2,
R 4.0.4, RASPA2 2.0.41, RDFlib 5.0.0, ReFrame 3.5.1, Ruby 2.7.2, rnaQUAST 2.2.0, SAMtools 1.12, SDL2 2.0.14,
SIMPLE 3.0.0, SPAdes 3.15.2, SUNDIALS 5.7.0, Seurat 4.0.1, Spark 3.1.1, scikit-image 0.18.1, silx 0.14.0,
spglib 1.16.1, sympy 1.7.1, tensorboardX 2.1, tensorflow-probability 0.12.1, tmux 3.1c, USEARCH 11.0.667,
VTK 9.0.1, VTune 2020_update3
- minor enhancements, including:
- verify checksum of all patch files in easyconfigs test suite (#12221)
- add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a (#12227)
- add sanity check commands for vorbis-tools (#12304)
- add extensions to R-bundle-Bioconductor 3.12: motifmatchr (#12390), OUTRIDER + FRASER (#12510)
- add DMCfun extension for R v4.0.3 + v4.0.4 (#12409)
- various bug fixes, including:
- add missing GNU time dependency to WRF 4.0.2 built with foss/2018b (#12179)
- add archive source_urls for Hadoop and Spark (#12220)
- add missing Python build dep for SeqAn 2.4.0 (#12222)
- add missing pkg-config build dependency to VCFtools 0.1.16 (#12245), GObject-Introspection-1.64.0 (#12298), libsndfile (#12303)
- set $HTSLIB_DIR in HTSlib for use by EnsEMBLCoreAPI & Bio-DB-HTS (#12253)
- bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0 (#12277, #12288)
- bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error (#12293)
- skip sanity check test in IPython-7.18.1-GCCcore-10.2.0.eb (#12294)
- add missing Perl and Autotools build dependencies in recent WRF easyconfigs (#12301)
- add missing groff build dependency for Perl 5.30.0 and 5.32.0 (#12307)
- add linkcomm + rnetcarto extensions to R v4.0.3 (#12311)
- add dependency on Flask in all ASE v3.21.1 easyconfigs (#12312)
- remove hard-coded -xHost from MMseqs2-11-e1a1c (#12317)
- revised outdated easyconfigs for libcerf + replaced obsolete homepages and source urls (#12323)
- consistently include 'new_archive' source URL in Qt5 easyconfigs + add missing checksums (#12325, #12426)
- fix source URL and add alternate checksum for Hypre 2.14.0 (#12337)
- add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI (#12340)
- add SourceForge fallback source URL for recent freetype easyconfigs (#12341)
- revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 (#12345)
- use -D_USE_METIS_5p1 in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0 (#12403)
- make sure that path to eb is always found by tests (#12436)
- stop tests changing the EasyBuild easyconfigs (#12454)
- use pip to install pkgconfig 1.5.1 (#12455)
- add CI test checking if the Python default source_urls are used and fix CI check where use_pip=False was ignored (#12456, #12471)
- fix source URLs in Arrow 0.x easyconfigs (#12475)
- fix numpy tests for recent SciPy-bundle easyconfig on POWER (#12481)
- don't download hwloc during FIRESTARTER build (#12482)
- avoid 0.0.0 install version for various Python apps (#12519, #12522)
- enable USER_SDPD package and disable building docs in LAMMPS 3Mar2020 (#12527)
- update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages (#12534)
- add Python 3 build dep for HMMER 3.3.x test step (#12536)
- other changes:
- rename opencv_contrib and update to OpenCV v3.4.1 with contrib versionsuffix (#12229)
- fix minor style issues in POV-Ray v3.7.0.8 easyconfigs (#12342)
- enable -fPIC for g2clib (#12349)
- consistently include Keras-Applications and Keras-Preprocessing extensions in Keras 2.3.1 easyconfigs (#12375)
- remove PYPI_SOURCE source URL from easyconfigs using PythonPackage or PythonBundle (#12541, #12452, #12453)
- require sanity_pip_check for all Python package/bundles (#12464)
v4.3.3 (February 23rd 2021)
---------------------------
update/bugfix release
- add easyconfig for new iibff toolchain: iibff/2020b (#12185)
- added easyconfigs for 6 new toolchains:
- gobff/2020b (#12098), goblf/2018b (#6615), gomkl/2020b (#12198), iimkl/2018a (#6092), iomkl/2019b (#11981), iomkl/2020b (#12009)
- added example easyconfig files for 72 new software packages:
- AOCC (#11868), CHERAB (#7141), CaDiCaL (#11966), CellRanger-ARC (#12114), CuPy (#11749), DFA (#11979),
FIGARO (#11924), FIRESTARTER (#12160), FIt-SNE (#8630), GPyTorch (#12010), GSEA (#10395), GetOrganelle (#11948),
Glucose (#11965), GraPhlAn (#10707), ITSx (#10558), Kaleido (#11998), LAPACK (#6615), LSD2 (#11903),
Lingeling (#11964), MPB (#7026), MiniCARD (#11963), MiniSat (#11962), NGSpeciesID (#11918), NanopolishComp (#11823),
Nsight-Compute (#12043), Nsight-Systems (#12042), PHANOTATE (#8667), PIPITS (#10558), PyClone (#11940),
PySAT (#12000), RNAmmer (#7262), Raysect (#7141), SICER2 (#12200), SOCI (#12045), SeisSol (#7194), SignalP (#11862),
Stack (#11310), SuperLU_DIST (#11693), Teneto (#12056), Transformers (#12032), YANK (#11742), Z3 (#12013),
bgen (#7456, #11867), bgen-reader (#7456, #11867), bpytop (#12040), byobu (#11932), chi2comb (#11867),
cuTENSOR (#11914), dd (#11978), decona (#11891), dicom2nifti (#11955), eccodes-python (#12083), fftlib (#11944),
flatbuffers-python (#12148), fpocket (#11980), gh (#11851), intel-compilers (oneAPI) (#11982), libGDSII (#7026),
libpci (#11871), liknorm (#7456, #11867), limix (#7456, #11867), logaddexp (#11867), neptune-client (#11985),
plinkQC (#12068), preCICE (#11886), py-aiger (#11999), py-aiger-bdd (#11999), pytest-xdist (#11883, #11893),
samblaster (#7378), terastructure (#12197), typing-extensions (#11636), webin-cli (#8674),
- added additional easyconfigs for various supported software packages, including:
- ack 3.4.0, AmberTools 20, AMD-LibM 3.6.0-4, AMD-RNG 2.2, AMD-SecureRNG 2.2, annovar 20191024, ASE 3.21.1,
AUGUSTUS 3.4.0, Bazel 3.7.2, bcgTree 1.1.0, BLAST+ 2.11.0, Bonito 0.3.5, Bowtie2 2.4.2, causalml 0.8.0-20200909,
CGAL 5.2, ConnectomeWorkbench 1.4.2, CUDAcore 11.2.1, cuDNN 8.0.5.39, dcm2niix 1.0.20201102, DendroPy 4.5.2,
DIAMOND 0.9.36 + 2.0.6, ecCodes 2.20.0, ELPA 2020.11.001, Emacs 27.1, FusionCatcher 1.30, gensim 3.8.3, GHC 8.6.5,
gnuplot 5.4.1, GPAW 21.1.0, Graphviz 2.44.1, GROMACS 2020.5, Gurobi 9.1.0, HH-suite 3.3.0, HMMER 3.3.2, HTSlib 1.11,
Horovod 0.21.1, imbalanced-learn 0.7.0, impi 2021.1.1, inferCNV 1.3.3, ITK 5.1.2, IQ-TREE 2.1.2, JasPer 2.0.24,
JUBE 2.4.1, libgit2 1.1.0, libzip 1.7.3, likwid 5.1.0, MariaDB 10.5.8, medaka 1.2.0, Meep 1.6.0, mkl-service 2.3.0,
MPICH 3.3.2, muParser 2.3.2, NanoComp 1.13.1, NanoPlot 1.33.0, networkx 2.5, NLTK 3.5, numba 0.52.0, NVHPC 20.11,
nvtop 1.1.0, OpenCoarrays 2.9.2, OpenFOAM v2012, OpenJPEG 2.4.0, OpenMPI 4.1.0, parasail 2.4.2, PLUMED 2.6.2,
PostgreSQL 13.2, pydicom 2.1.2, PyMC3 3.11.0, python-parasail 1.2.2, PyTorch 1.7.1, QIIME2 2020.11,
QuantumESPRESSO 6.7, QuickFF 2.2.7, R 4.0.3, R-bundle-Bioconductor 3.12, ReFrame 3.4.1, RMBlast 2.10.0, RSEM 1.3.3,
Salmon 1.4.0, scikit-build 0.11.1, SciPy-bundle 2020.03 w/ Python 2.7.18, Seaborn 0.11.1, SEPP 4.4.0,
SHAPEIT4 4.2.0, SpaceRanger 1.2.2, Stacks 2.54, STAR 2.7.7.a, statsmodels 0.12.1, SuiteSparse 5.8.1, tbb 2020.3,
TensorFlow 1.15.5 + 2.4.1, Theano 1.1.2, torchvision 0.8.2, V8 3.4.0, Wannier90 3.1.0
- minor enhancements, including:
- enable building of QtWebEngine in Qt5 easyconfig using foss/2017b or intel/2017b (#7302)
- enable NVPTX offload in GCCcore 9.3.0 easyconfig (#11839)
- also build shared library in recent HDF easyconfigs (#11847)
- add support for HDF4 to GDAL v3.0.2 and v3.0.4 (#11855)
- add patch for magma 2.5.4 with fosscuda/2019b to allow any sm_* value to be passed via GPU_TARGET (#11861)
- add missing M4 build dependency to recent SuiteSparse versions (#11869)
- enable tests for most recent Bazel versions (3.x) (#11894)
- enable gipaw in QuantumESPRESSO 6.6 easyconfig (#11905)
- add RCAL + sensemakr extensions to R 4.0.0 (#11921)
- add additional extensions to R v4.0.3 easyconfig (#11922, #12057)
- improve sanity_check_paths for AMD-LibM (#11933)
- symlink include/lib subdirs + enhance sanity_check_paths for AMD-RNG v2.2-4 (#11934)
- improve sanity_check_paths for AMD-SecureRNG (#11935)
- update Clang 10+ dependencies & build extra tools (#12013)
- add Inline extension to recent Perl easyconfigs (5.30+) (#12029)
- add EnsDb.Hsapiens.v86 to Bioconductor 3.11 (#12078)
- add sanity check command for bam-readcount v0.8.0 to check --version output (#12092)
- add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 (#12174)
- add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (#12136, #12137)
- various bug fixes, including:
- added missing space in 'configopts' in ParaView 5.8.0 easyconfigs using 2020a toolchain (#10989)
- use bfd linker for glibc 2.30 (#11331)
- add missing moduleclass in UCLUST easyconfig (#11477)
- don't disable optarch for Clang 11.0.0 (#11814)
- add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x (#11837)
- fix compilation of TensorFlow 2.3.1 with CUDA and glibc 2.26 on POWER (#11859)
- disable building of manpages for GDCM to fix installation problem with docbook (#11866)
- add patch for LLVM 6.0.0 to fix missing exported symbol LLVMInitializeInstCombine (#11873)
- fix name of source file for GDRCopy v2.1 (#11887)
- fix Tombo to work with rpy2 v3 when creating DataFrames (#11892)
- fix GCCcore 8.1.0 w.r.t. removed sys/ustat.h in glibc 2.28 (#11896)
- add git as a dependency to GitPython version 3.x (#11902)
- fix undefined __ieee128 on ppc64le with glibc 2.26 for magma (#11930) and PyTorch (#11936)
- update Hypre git location for PETSc 3.11.0 using downloaded dependencies (#11947)
- fix source URL in expat easyconfigs (and consistently add custom sanity_check_paths) (#11960)
- use libpng provided by EasyBuild in VTK to fix build issue on ppc64le (#11990)
- add missing pkg-config build dependency for GObject-Introspection v1.66.1 (#11949)
- add missing plotly-orca dependency for NanoPlot (#11967, #12015)
- add patch for Boost 1.74.0 to fix missing include file (#12007)
- fix for "error: 'runtime_error' is not a member of 'std'" in qtlocation for Qt5 v5.14.2 (#12012)
- fix homepage for gnuplot 5.2.8, use http:// since homepage is not reachable via https:// (#12047)
- fix OS dependencies for libfabric (#12058)
- fix vector mul and div with broadcasts in -masm=intel mode in GCCcore v9.3.0 (#12065)
- add missing ESMF dependency in NCO easyconfigs (#12071, #12072)
- add patch to fix version for bam-readcount 0.8.0 (#12075)
- add missing Perl build dep for (recent) libcerf versions, required for 'pod2html' command (#12085)
- add missing bzip2 dependency to recent ncbi-vdb easyconfigs (#12120)
- add missing Perl build dependency for BLIS 0.8.0 (#12146)
- use https://sources.easybuild.io as fallback source URL for UDUNITS (#12049, #12156, #12182)
- correct the GCC version check to allow IBM VSX builds of GROMACS 2020.4 and 2020.5 (#12159)
- add missing mkl-service dependency for Theano built with intel/2019b + enhance sanity check (#12172)
- add patches to fix test problems with p4est 2.2 (#12028)
- fix build of Bison using older system GCC (v4.x) (#12203)
- fix lack of optimisation for SHAPEIT4 v4.1.3 (#12206)
- add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6 (#11801, #12208)
- fix source URL for libspatialite (#12213)
- add 'archive' fallback source URL to MAGMA easyconfigs (#12214)
- fix checksum for patch in make 4.2.1 easyconfig using GCC/7.3.0-2.30 (#12223)
- other changes:
- replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a single easyconfig for BioPP v2.4.1 (using Bundle easyblock) (#11609)
- add CESM-deps to whitelist in check for custom sanity_check_paths (#11916)
- include '-4' in version for AMD-SecureRNG v2.2-4 (#11934, #11935)
- switch to using python-parasail and tqdm dependencies in Bonito easyconfigs (#11937)
- rename orca to plotly-orca (#12015)
- remove duplicate extensions in R 3.5.x easyconfigs, and add test to detect such issues (#12059)
- remove Python dependency from ecCodes v2.17.0 since it doesn't provide Python bindings (#12084)
- update Java/1.8 wrapper to Java 1.8.0_281 (#11928, #12088)
- update Bison (build) dependency for flex built with system compiler to v3.5.3 (#12111)
- make symlinking of posix.so in test suite configuration conditional (#12123)
- move make 4.3 easyconfigs to GCCcore toolchain (#12166)
- move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore (#12168)
- rename SNAP to SNAP-HMM and update easyconfig (#12218)
v4.3.2 (December 10th 2020)
---------------------------
update/bugfix release
- add easyconfigs for new gobff toolchain: gobff/2020.11 + gobff/2020.06-amd (#11761)
- add easyconfigs for updates of common toolchains: foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added example easyconfig files for 41 new software packages:
- alsa-lib (#11658), assimp (#11759), BioServices (#11602), carputils (#11270), cctools (#11799),
code-server (#11778), CRISPResso2 (#11775), elfutils (#11783), EMU (#11641), fgbio (#11519), Flink (#11747),
FreeSASA (#11699), Geant4-data (#11610), geocube (#11714), IPM (#11768, #11772), libmicrohttpd (#11783),
libStatGen (#7982), libzeep (#11687), LLDB (#11822), meshalyzer (#11270), meshtool (#11270),
Metagenome-Atlas (#11620), MLxtend (#11601), MRChem (#11604), MRCPP (#11579), mxml (#11769), mxmlplus (#11771),
nanocompore (#11690), neon (#11797), Open-Data-Cube-Core (#11713), OpenSees (#11613), PEST++ (#11565),
pyFAI (#11849), pymca (#11848), RE2 (#11718), scikit-bio (#11660), SpaceRanger (#11776), SplAdder (#11607),
SWAT+ (#11615), velocyto (#11744), WCT (#11779)
- added additional easyconfigs for various supported software packages, including:
- BBMap 38.87, Boost 1.74.0, CUDA 11.1.1, CellRanger 5.0.0.eb, CheckM 1.1.3, Clang 11.0.0, cuDNN 8.0.4.30,
DMTCP 2.6.0, FDS 6.7.5, FFmpeg 4.3.1, GROMACS 2020.4, Geant4 10.6.2, Ghostscript 9.53.3, GitPython 3.1.9,
GlobalArrays 5.8, HDF5 1.10.7, h5py 3.1.0, hypothesis 5.41.5, JasPer 2.0.16, LittleCMS 2.11, libedit 20191231,
libyaml 0.2.5, MPFR 4.1.0, magma 2.5.4, matplotlib 3.3.3, NCCL 2.8.3, NLopt 2.6.2, Nextflow 20.10.0,
netCDF-Fortran 4.5.3, OpenBLAS 0.3.12, OpenMolcas 20.10, Pillow 8.0.1, PnetCDF 1.12.1, PyYAML 5.3.1,
packmol 20.2.2, protobuf 3.14.0, psycopg2 2.8.6, pybind11 2.6.0, pycocotools 2.0.2, Qt5 5.14.2, RAxML-NG 1.0.1,
RSeQC 4.0.0, rioxarray 0.1.1, SCOTCH 6.1.0, SciPy-bundle 2020.11, SentencePiece 0.1.94, StringTie 2.1.4,
SuperLU 5.2.2, scikit-learn 0.23.2, snakemake 5.26.1, tqdm 4.51.0, vsc-mympirun 5.2.5, x264 20201026
- minor enhancements, including:
- add extension to R-bundle-Bioconductor 3.11: snpStats (#11586), SCANVIS (#11638)
- add extensions to R 4.0.0: coloc, Exact, lmom, gld, DescTools (#11587); nlsem (#11733); mitools, survey, tableone, jstable (#11841)
- add gxmapi extension (Python bindings) to GROMACS 2020.4 (#11640)
- add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs (#11654)
- enable NVPTX offload support in GCCcore 10.2.0 easyconfig (#11720)
- various bug fixes, including:
- prevent Minimac4 easyconfig from downloading libStatGen from GitHub (#7982)
- limit build parallelism for RAxML-NG to avoid build failure (#10363)
- fix source_urls in Geant4 easyconfigs (#11596)
- add alternate checksum for extensions in R easyconfigs: KernSmooth (#11600), codetools (#11616, #11736)
- fix BBMap version check in FusionCatcher v1.20 (#11608)
- add patch for TensorFlow 2.3.1 to fix installation on Arm64 (#11614)
- add patch for GCCcore 10.2 to fix __has_include regression (#11627)
- change default bitmaptype for IRkernel to cairo (#11645)
- set $JUPYTER_PATH to make Jupyter find the ipywidgets extension in recent IPython easyconfigs (#11649)
- add missing dependencies + fix moduleclass in CheckM easyconfigs (should be bio) (#11662)
- use Python 2 build dep for nodejs 12.19.0 (#11679)
- use correct OS deps in UCX (#11702)
- in-place update to magma 2.5.4 for PyTorch 1.2.0 (#11723)
- in-place update to magma 2.5.4 for PyTorch easyconfigs using fosscuda/2019b toolchain (#11726)
- add missing Java dep to Prokka (#11732)
- add patch to fix possible memory leak in OpenBLAS 0.3.3+ (#11745)
- do not treat warnings as errors in Java v1.8_191-b26-OpenJDK (POWER) (#11755)