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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 http://easybuild.readthedocs.org/en/latest/Release_notes.html.
The latest version of easybuild-easyconfig provides 10,147 easyconfig files, for 2,013 different software packages,
incl. 31 different (compiler) toolchains.
v4.2.2 (July 8th 2020)
----------------------
update/bugfix release
- added easyconfigs for 2 new toolchains:
- golf/2020a (#10672)
- intel/2020.06, based on intel/2020a but with impi 2018 update 5 (#10864)
- added example easyconfig files for 36 new software packages:
- AmrPlusPlus (#9919), arrow (#10882), attrdict (#10827), Cartopy (#10685), dm-tree (#10775), dotNET-SDK (#10661),
FLAIR (#10860), fastqsplitter (#10706), GLFW (#10709), git-extras (#10440), hl7apy (#10728), hyperopt (#10735),
IgBLAST (#10889), IntelDAAL (#9848), ichorCNA (#10595), MARS (#10691), MITObim (#10897), MUST (#10849),
mhcnuggets (#9743), PAUP (#10830), Percolator (#10665), PyBerny (#10885), poetry (#10884), pycocotools (#10806),
python-hl7 (#10673), SHAPEIT4 (#10814), SYMPHONY (#10058), SunPy (#10676), sdsl-lite (#10691),
TEtranscripts (#10909, #10921), Tombo (#10646), tensorboardX (#10774), Unidecode (#10828), WHAM (#10736), XALT (#9792),
Xvfb (#10512)
- added additional easyconfigs for various supported software packages, including:
- Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, Blitz++ 1.0.2,
Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10,
dask 2.18.1, Elk 6.3.2, GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6,
geopandas 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0,
IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, MATIO 1.5.17,
MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 2.10.5, NiBabel 3.1.0,
Nipype 1.4.2, ncbi-vdb 20.10.7, numba 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006,
PDT 3.25.1, PRSice 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2,
Pysam 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1,
ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 1.3.959,
SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, Seaborn 0.10.1,
Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, StringTie 2.1.3, scikit-allel 1.2.1,
scikit-learn 0.23.1, snpEff 4.3t, Valgrind 3.16.1, VarScan 2.4.4,
vsc-mympirun 5.1.0, WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0
- minor enhancements, including:
- add extensions to R 4.0.0 easyconfig: drgee + stdReg (#10833), copCAR (#10911), ngspatial (#10913), drugCombo (#10914)
- add extensions to R-bundle-Bioconductor 3.11 easyconfig: BSgenome.Cfamiliaris.UCSC.canFam3 (#10840), SingleR (#10904)
- include extra extension and support for MPI in MAFFT v7.453 and v7.470 (#10853)
- add Array::Transpose to Perl (#10878)
- various bug fixes, including:
- fix dependencies and configuration of CoinUtils ecosystem (#10450)
- fix Togl configure patch so that it completely ignores TCL_SRC_DIR and TK_SRC_DIR (#10662)
- change Xerces-C++ to official CMakeMake build (fixes missing links to curl) (#10664)
- add -fPIC to toolchainopts in easyconfig for Lua 5.3.5 with system toolchain (#10671)
- remove hardcoded X86 target in LLVM easyconfigs (#10677)
- switch to https homepage and source_urls in libGLU easyconfigs (#10686)
- add patch for h5py 2.10.0 to avoid triggering MPI_Init at import (#10687)
- add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (#10692)
- update UDUNITS source_urls to https sources (#10693)
- add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (#10695, #10697)
- add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (#10710)
- add M4 builddependency to SuiteSparse 2019b easyconfigs (#10720)
- make sure WHAM is built with correct compiler (#10736)
- define MAX_JOBS in easyconfigs of PyTorch from v1.1.0 to v1.4.0 (#10772)
- add dm-tree and lz4 as dependencies to Ray v0.8.4 (#10775)
- fix source URL in recent ant easyconfigs (#10790)
- bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in Bioconductor 3.11 bundle, since sources for old versions have disappeared (#10791)
- add patch to Armadillo easyconfigs using the foss toolchain to prevent it from picking up MKL if installed system-wide (#10812)
- add missing kerneltree extension in FLAIR easyconfig (#10860)
- fix source URLs in Eigen 3.2.* (#10872) and 3.3.* (#10869) easyconfigs
- refer to issue in GitHub repo in configparser patch, since Bitbucket repo is disappearing (#10873)
- switch to github.com source URL for MetaPhlAn (#10874)
- switch to GitHub sources for ScientificPython 2.9.4 (#10875)
- switch to GitHub source URL for HPDBSCAN (#10876)
- download x265 3.2/3.3 sources from bitbucket.org/multicoreware/x265_git (#10905)
- fix download URL for libatomic in gc 7.6.12 easyconfigs (#10915)
- fix sanity_check_paths in CFITSIO-3.48-GCCcore-9.3.0.eb easyconfig (#10917)
- add missing dependencies for geopandas 0.7.0 (#10923)
- other changes:
- rename OpenPyXL 2.6.4 easyconfig to openpyxl (#10916)
v4.2.1 (May 20th 2020)
----------------------
update/bugfix release
- added easyconfigs for new common toolchains: foss/2020a (#10483, #10492), intel/2020a (#10494)
- added example easyconfig files for 66 new software packages:
- Alpha (#9994), antiSMASH (#10589), Arlequin (#10620), artic-ncov2019 (#10459), augur (#10405), AutoMap (#10419),
Bio-EUtilities (#10037), CaSpER (#10593), cdbfasta (#10547), cddlib (#10429), CoCoALib (#10429)
dftd3-lib (#10351), DoubletFinder (#10603), E-ANTIC (#10429), FastViromeExplorer (#10571), FIX (#8870),
FusionCatcher (#10134), geopandas (#10322), goalign (#10469), gotree (#10459), gretl (#10413), harmony (#10604),
HDF-EOS (#10534), HDF-EOS5 (#10536), HMMER2 (#10588), HyPo (#10642), king (#10365), libdeflate (#10459),
libfabric (#10616), libgit2 (#10453), libuv (#10444), mbuffer (#10524), MDAnalysis (#10545), MEM (#10605),
MESS (#10597), metaerg (#10037), MinCED (#10037), MitoZ (#7735), nauty (#10429), nifti2dicom (#10598),
NLMpy (#10029), ntCard (#10502), NTL (#10431), pIRS (#10508), popscle (#10550), ProtHint (#10549),
protozero (#10495), pysndfx (#10452), PyVCF (#10564), PyWavelets (#10501), rampart (#10459), rickflow (#10641),
RNA-Bloom (#10502), root_numpy (#10424), rstudio (#10619), ScaFaCoS (#10537), Scythe (#10524), SDSL (#10642),
SHAP (#10379), SNPomatic (#10524), SoX (#10452), swissknife (#10037),) Taiyaki (#10573), TCLAP (#10598),
torchaudio (#10516), wtdbg2 (#10524)
- added additional easyconfigs for various supported software packages, including:
- ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4,
CPLEX 12.10, CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 2.17.0, expat 2.2.9, FFmpeg 4.2.2,
FriBidi 1.0.9, GATK 4.1.5.0, GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 6.2.0, GROMACS 2020.1,
GTK+ 3.24.17, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2,
gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1,
IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1,
libarchive 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 2.0.4, librsvg 2.48.4, libsigsegv 2.12,
lrslib 7.0a, MEME 5.1.1, MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 1.3.1, MultiQC 1.8,
matplotlib 3.2.1, NGS-Python-2.10.4, NGS 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1,
Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1,
OpenMPI 4.0.3, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PLUMED 2.6.0, PMIx 3.1.5,
PROJ 7.0.0, Perl 5.30.2, Pillow 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 5.14.1,
R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3,
rioxarray 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 2.0.10, SIONlib 1.7.6, SQLite 3.31.1,
SRA-Toolkit 2.10.4, Salmon 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, StringTie 2.1.1,
SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2,
tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12,
wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, zstd 1.4.4
- minor enhancements, including:
- add additional extensions for recent versions of R (#10359, #10585, #10586, #10621) and R-bundle-Bioconductor (#10585, #10596, #10621)
- add additional extensions for recent versions of Perl (#10412, #10546, #10623)
- include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(#10458)
- include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (#10464)
- add alternate checksum for EMBOSS (#10607)
- various bug fixes, including:
- fix incorrect checksums for Amber patches (#8870)
- add patches to fix installation of R 3.6.2 on POWER (#9830)
- add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380)
- add Perl as a build dependency for recent Autoconf/Automake easyconfigs (#10408, #10426)
- fix source_urls in ICU easyconfigs (#10417)
- disable USER-INTEL package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (#10418)
- fix undefined reference to 'qfloat16::mantissatable' in Qt5-5.13.1-GCCcore-8.3.0 (#10425)
- get rid of double '-' in versionsuffix of torchtext easyconfig (#10472)
- fix broken Mako easyconfigs (#10480, #10627)
- move builddependencies to dependencies in OTF2 and Score-P easyconfigs (#10496)
- add missing cURL dep for LAMMPS (#10527)
- add Python 2 build dependency for OpenPGM (#10539)
- use OS_PKG_IBVERBS_DEV constant for OS dependency in PyTorch 1.4.0 easyconfigs (#10540)
- add missing Bison build dep in Graphviz easyconfigs (#10541)
- use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (#10559)
- add missing PyVCF dependency for BAMSurgeon (#10564)
- remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (#10565)
- fix ITK v5.0.1 easyconfig w.r.t. locale and location of libjpeg-turbo library (#10592)
- add patch to fix missing const qualifiers for ncurses (#10606)
- fix OS dependency for rstudio for Debian-based systems (#10608)
- fix Rmath paths in easyconfig for FastQTL v2.184 (#10612)
- add symlink for Arlequin commands + fix sanity check commands (#10620)
- fix recent binutils easyconfigs usign system toolchain for Fedora 32 / GCC 10 (#10633)
- replace '/path/to' with actual installation prefix in FuSeq scripts (#10640)
- other changes:
- check sdist with different Python versions in CI (#10388)
- use Bison 3.3.2 as build dep for flex 2.6.4 (#10403)
- mention http:// Pfam website rather than ftp:// in load message of BiG-SCAPE easyconfig (#10439)
- archive old Singularity configs (#10591)
- Singularity is not well suited to install via EasyBuild because it requires admin privileges to enable setuid
- stop using old hpcugent URL for cloning framework/easyblocks repos in CI (#10635)
- use SYSTEM constant for toolchain in easyconfigs already use 'system' toolchain (#10638)
v4.2.0 (April 14th 2020)
------------------------
feature release
- added example easyconfig files for 114 new software packages:
- ABRA2 (#10272), ABRicate (#10310), ADIOS (#10036), aNCI (#9929), any2fasta (#10310), apex (#10269),
archspec (#9898), ArviZ (#10366), autopep8 (#9626), BAMSurgeon (#10330), BatMeth2 (#10323),
BiG-SCAPE (#10352), BinSanity (#10001), Bonito (#10269), BSMAPz (#10283), BSseeker2 (#10039),
BUStools (#9838), Cbc (#10052), Cgl (#10048), CGmapTools (#10288), Clp (#10033), CoinUtils (#9937),
dtcwt (#9695), ELSI (#9857), EnsEMBLCoreAPI (#8734), fastq-pair (#9894), FigureGen (#10076), Fiona (#10321),
FuSeq (#10004), GenomeTools (#9797), GraphMap2 (#10299), GRASP (#9896), Groovy (#9809), gsport (#9821),
gubbins (#9689), igv-reports (#9977), inferCNV (#9686), iVar (#10291), joypy (#10212), JupyterLab (#9752),
kma (#10259), LAMMPS (#10371), lancet (#10271), libBigWig (#10006), libGridXC (#9858), libPSML (#5859),
LtrDetector (#10343), manta (#5104), medImgProc (#10228), MedPy (#9748), Mini-XML (#10036), mkl_fft (#9887),
Monocle3 (#9825), MoreRONN (#10255), motionSegmentation (#10228), NanoComp (#10212), NanoFilt (#10212),
nanoget (#10212), nanomath (#10212), NanoPlot (#10212), ngspice (#9922), ntEdit (#9836), ntHits (#9833),
occt (#9939), OCNet (#9955), OpenAI-Gym (#10347), OpenPIV (#9959), OpenPyXL (#10115), orca (#9518),
Osi (#10361), PartitionFinder (#9983), pauvre (#10212), polymake (#9904), pretty-yaml (#10041)),
PRSice (#9988), pycodestyle (#9626), pydot (#9899), pygraphviz (#9969), pylift (#10051), PyMC3 (#10279),
pyparsing (#9983), PyRe (#10095), python-weka-wrapper3 (#9704), PyTorch-Geometric (#9995), qcat (#10244),
RAxML-NG (#9990), Ray (#10302), rclone (#7934), Red (#9856), rstanarm (#9964), scikit-build (#9762),
scVelo (#9805), SECAPR (#9721), segmentation-models (#10211), SentencePiece (#10192), SEPP (#10047),
Shapely (#10309), Singular (#10030), SLATEC (#7529), spatialreg (#9767), split-seq (#9749), spoa (#9705),
SSN (#9955), STEAK (#10337), stpipeline (#9736), SVG (#9905), Togl (#9868), torchtext (#10193),
units (#9682), UQTk (#10279), WildMagic (#10044), Winnowmap (#10005), xtb (#9993), Zip (#9972)
- added additional easyconfigs for various supported software packages, including:
- ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34,
CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8,
DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1,
GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020,
GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1,
gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1,
Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166,
ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045,
LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453,
MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0,
Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1,
Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11,
PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1,
pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3
Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0,
SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0,
SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0,
TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2,
tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4,
- minor enhancements, including:
- add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (#9371)
- add additional extensions for R: HiddenMarkov (#9685), lmerTest (#9853), VSURF + Rborist (#10355)
- change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (#9764)
- build shared libs and install header files for Ghostscript (#9785)
- add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, #9891)
- add Perl extensions: Term::ReadLine::Gnu (#9901), URI::Escape and Set::IntervalTree (#10049)
- add dat directory to aNCI (#9929)
- add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (#10045)
- build SUNDIALS with 'pic' (#10278)
- add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (#10298)
- fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (#10367)
- update Java/1.8 wrapper to Java/1.8.0_241.eb (#10305)
- various bug fixes, including:
- use CMake for building double-conversion (#9659)
- update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (#9694)
- add alternate checksum for OpenMolcas 18.09 (#9701)
- use Github to download releases for MariaDB-connector-c (#9702)
- add -DOMPI_SKIP_MPICXX in configopts for MathGL, to avoid using mpicxx during build (#9703)
- make installing independent of build folder in pybind11 easyconfig (#9738)
- add Lua as a dependency to gnuplot (#9773)
- stick to http:// source URLS for ISL in GCCcore easyconfigs, since https:// doesn't work (#9784)
- add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (#9789)
- add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (#9865)
- revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (#9866)
- fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (#9867)
- add missing sanity_check_commands to cutadapt v1.18 and v2.7 easyconfigs (#9869)
- don't overwrite configopts in BLAST+ easyconfigs, append to it (#9875)
- add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, #10382)
- fix redefining of preconfigopts in OpenCV easyconfigs (#9895)
- use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (#9912)
- fix NCIPLOT build flags (#9915)
- add missing patch to iccifort libxc easyconfigs (#9918)
- use checkout@v2 in GitHub Actions to fix broken re-triggered tests (#9925)
- re-enable building utils in Siesta 4.1-MaX-1.0 release (#9936)
- fix homepage and source URLs in SLEPc easyconfigs by using https (#9943)
- fix source URLs for rgeos after source tarball was moved to CRAN archive (#9954)
- add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (#9957)
- patch GCC lisanitizer for glibc 2.31 (#9966)
- add Zip as build dependency for recent Bazel versions (#9972)
- fix checksums in Jellyfish v2.3.0 easyconfigs (#9997)
- fix source URLs for ParMGridGen easyconfigs (#10019)
- disable unintended Octave support in all libsndfile easyconfigs (#10027)
- fix sources for LS-PrePost 4.6 (#10236)
- security update for vsc-mympirun 4.1.9 (#10185)
- configure libwebp to also install libwebpmux (#10274)
- ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (#10326)
- fix undefined reference error due to libxc 4.3.4 built with CMake (#10356)
- fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (#10361)
- update checksums and homepage in tbb easyconfigs (#10285)
- other changes:
- use new custom easyblock in recent CMake easyconfigs (#9871, #9923)
- add check for redefined easyconfig parameters in easyconfig tests (#9876)
- use M4-1.4.18.eb for test installation in easyconfigs test suite (#9926)
- use https in homepage/source_urls of zlib-1.2.11.eb (#10018)
- add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (#10083)
- add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (#10237)
- add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (#10276)
v4.1.1 (January 16th 2020)
--------------------------
update/bugfix release
- added example easyconfig files for 27 new software packages:
- Autoconf-archive (#9658), breseq (#9603), CrossMap (#9483), CSBDeep (#9560), CNT-ILP (#9323), cytoolz (#9453), Faber (#9553),
Fiji (#8748), GARLI (#9404), Globus-CLI (#9565), GtkSourceView (#9526), gradunwarp (#9648), gsettings-desktop-schemas (#9529),
HyPhy (#9405), horton (#7449), IGMPlot (#9438), LEMON (#9323), Meld (#9530), mhcflurry (#9554), NCIPLOT (#9419), ncl (#9632),
OpenSlide (#9499), openslide-python (#9499), pythran (#9488, #9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381)
- added additional easyconfigs for various supported software packages, including:
- Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2,
GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10,
lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13,
OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1,
pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0,
SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2,
WPS 4.1, WRF 4.1.3
- added easyconfigs for intel/2020.00 toolchain (#9575)
- minor enhancements, including:
- add POWER9 support to CUDA 10.1 easyconfigs (#9442)
- build CMake in parallel (#9543)
- use NCCL for GPU ops in Horovod 0.18.2 easyconfig (#9562)
- update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (#9585)
- various bug fixes, including:
- fix remote launch of broker and workers for SCOOP (#9366)
- fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388)
- add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain (#9424)
- add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (#9454)
- fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (#9455)
- fix CMake 3.15.3 build on Power (+ enable building in parallel) (#9469)
- fix source URLs in xorg-macros easyconfigs (#9477, #9578)
- add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (#9479)
- remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS in various easyconfigs (#9528, #9577, #9615)
- use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (#9546)
- fix lpsymphony extension for R-bundle-Bioconductor (#9548)
- add correct 'old-versions' source URL to all Mesa easyconfigs (#9569)
- add missing SHA256 checksums for Armadillo (#9572)
- also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS (#9579)
- add SSL OS dependencies for GDAL 3.0.0 (#9586)
- add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (#9587)
- patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (#9590)
- patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (#9591)
- fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (#9601)
- use absolute path for extraction to allow relocating the build dir for g2log-1.0 (#9604)
- add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (#9611)
- add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (#9621)
- update ctffind website (#9622)
- make sure we use easybuild Clang in pocl easyconfigs (#9624)
- make postinstallcmds independent of current working directory in OpenCV 3.1.0 easyconfigs (#9628)
- update source_urls to include old releases folder in libsodium easyconfigs (#9632)
- fix source URLs for ant v1.10.5 - v1.10.7 (#9633)
- update URLs to new location of libxc (#9635)
- add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (#9644)
- update source URLs in QCA 2.1.0 easyconfigs (#9647)
- fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI) (#9649)
- fix tesseract 4.1.0 dependencies (#9650)
- make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (#9652)
- use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters (#9657)
- fix pyfits easyconfig by adding missing d2to1 extension (#9687)
- other changes:
- disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492)
- require that sanity_pip_check is enabled in new/changed easyconfigs (#9516, #9576)
- update copyright statements for 2020 (#9598)
- allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (#9634)
v4.1.0 (December 4th 2019)
--------------------------
update/bugfix release
- added example easyconfig files for 46 new software packages:
- Amara (#9340), anvio (#9387), Arriba (#9226, #9244), attr (#7824), bibtexparser (#9284), bwa-meth (#9217), CITE-seq-Count (#9237),
CoordgenLibs (#9374), dtcmp (#9052), fatslim (#9193), GromacsWrapper (#9177), GULP (#9243), hdf5storage (#9195),
ITSTool (#7260), kim-api (#8786), kwant (#9238), libarchive (#9052), libcircle (#9052), libxml2-python (#7260),
lifelines (#9215), lwgrp (#9052), maeparser (#9374), MaxQuant (#9281), MethylDackel (#9216), MoviePy (#9205),
mpifileutils (#9052), mpiP (#9059), nanofilt (#8502), NOVOPlasty (#9326), openkim-models (#8786), parallel-fastq-dump (#9218),
pasta (#9348), pyqstem (#9277), python-Levenshtein (#9237), RapidJSON (#9373), RDFlib (#9346), RQGIS3 (#9125),
Short-Pair (#9376), SpliceMap (#9375), TRIQS-cthyb (#9230), TRIQS-dft_tools (#9230), TRIQS-tprf (#9230),
UMI-tools (#9237), VarDict (#7283), Xmipp (#9257), XSD (#9347)
- added additional easyconfigs for various supported software packages, including:
- awscli 1.16.290, BLIS 0.6.0, Bazel 1.1.0, Biopython 1.75, Blender 2.81, bokeh 1.4.0, CONCOCT 1.1.0, CUDA 10.2.89,
Catch2 2.11.0, CellRanger 3.1.0, CheckM 1.0.18, dask 2.8.0, deepTools 3.3.1, FastANI 1.2, Flye 2.6, GDCM 3.0.4,
GTDB-Tk 0.3.2, Glade 3.8.6, Hadoop 2.9.2, h5py 2.10.0, hypothesis 4.44.2, IPython 7.9.0, Kaiju 1.7.2, Kraken 1.1.1,
libsodium 1.0.18, MEGAHIT 1.2.8, Mesa 19.2.1, MetaBAT 2.14, matplotlib 3.1.1, metaWRAP 1.2.2,cNCCL 2.4.8,
NGS 2.10.0, NiBabel 2.5.1, netCDF 4.7.1, networkx 2.4, numba 0.46.0, OpenCV 3.4.7, OpenCoarrays 2.8.0, OpenEXR 2.4.0,
OpenFOAM v1906, OpenImageIO 2.0.12, ParaView 5.6.2, Pillow 6.2.1, PyTorch 1.3.1, PyYAML 5.1.2, Pysam 0.15.3,
picard 2.21.1, prokka 1.14.5, protobuf 3.10.0, R-keras 2.2.5.0, Racon 1.4.7, SCOTCH 6.0.9, SRPRISM 3.1.1,
Salmon 0.14.2, SciPy-bundle 2019.10, Subread 2.0.0, scikit-image 0.16.2, scikit-learn 0.21.3, TRIQS 2.2.1,
TensorFlow 1.15.0, TensorFlow 2.0.0 w/ fosscuda/2019b, Tkinter 3.7.4, ToFu 1.4.1, tbb 2019_U9, Xerces-C++ 3.2.2,
Xmipp 3.19.04, yaff 1.6.0
- added easyconfigs for intelcuda/2019b toolchain (#9271)
- minor enhancements, including:
- tweak Java 1.8 wrapper to use different Java version on POWER systems (#9081)
- add jupyter_nbextensions_configurator extension to IPython 7.7.0 easyconfigs (#9133)
- add additional extensions to R 3.6.0 easyconfigs (#9184, #9275)
- add additional extensions to R-bundle-Bioconductor 3.9 easyconfig (#9185, #9349, #9410)
- enhance sanity check in cutadapt 1.18 easyconfigs + consistently use PythonBundle & use_pip (#9219)
- update cuDNN 7.6.4.38 easyconfigs to support both x86_64 and ppc64le (#9331)
- tweak NCCL 2.4.8 easyconfig to support x86_64 and ppc64le (#9336)
- define $SPARK_HOME in generated module file for Spark 2.4.0 (#9408)
- add sanity check command for matplotlib 3.x with Python 3 to check import from mpl_toolkits (#9413, #9414)
- various bug fixes, including:
- explicitly set SYSCONFDIR configure option in TurboVNC easyconfig (#9137)
- patch pigz Makefile so zlib provided by EasyBuild is picked up (#9138)
- add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, to avoid picking up LibTIFF installed in system (#9146)
- add freetype as dependency to OpenImageIO, to avoid picking up freetype installed in system (#9147, #9152)
- fix definition of fosscuda/2019b to make sure it works with hierarchical MNS (#9178)
- add missing setuptools_scm extension required to build dateutil extension in Python 3.7.0 easyconfigs (#9209)
- add Python as build dependency for recent Bazel versions (#9223, #9299, #9342)
- fix homepage & description in Bioconductor easyconfigs (#9225)
- fix checksum in Stacks 2.41 easyconfig after sneaky re-release (#9232)
- apply fixes to ImageJ 1.51k easyconfig (#9245)
- consistently use patch for OpenCV 3.4.7 (#9279)
- use protobuf 3.10.0 as build dep for TensorFlow 2.0.0 w/ fosscuda/2019b + use nodocs variant of git as build dep (#9298)
- add Jasper dependency to Qt5 v.5.13.1 (#9313)
- fix Python 3.7.2 required OpenSSL version for old OS to the one provided on the same toolchain (#9324)
- add missing extensions required by Sphinx & pytest to easyconfigs for Python 3.7.2 and 3.7.4 (#9329)
- update TensorFlow v1.14.0 + v2.0.0 CUDA patch to handle compiler wrappers like ccache (#9333)
- patch binutils 2.31.1 and 2.32 to fix compatibility with RHEL8 (#9335)
- add missing extensions in TensorFlow 2.0.0 easyconfigs (+ update to tensorboard/tensorflow-estimator 2.0.1) (#9338)
- fix logic to determine location of scripts dir + ensure right compiler flags are used in KAT easyconfigs (#9360)
- add missing GCCcore-6.3.0_fix-sanitizer_linux.patch in GCCcore 6.4.0 easyconfig (#9362)
- fix linker errors when linking with libhts.a for MetaBAT 2.12.1 (#9379)
- add egg-info file via patch in VTK v8.2.0, for Pytho 2.7.15, 3.7.2, 3.7.4 (#9386)
- promote binutils to a runtime dependency for Python in GCCcore based builds (#9402)
- fix archive URL typo for ncdf4 (#9407)
- fix problems with mpl_toolkits namespace for matplotlib easyconfigs using Python 2 (#9415, #9416, #9417)
- other changes:
- ignore commented out lines in easyconfig files when checking for http:// URLs (#9224)
- add GitHub Actions workflow to run easybuild-easyconfigs test suite (#9231, #9255)
- archive old patches for Xmipp 3.1 (#9256)
- speed up easyconfigs test suite by avoiding re-parsing and re-ordering of easyconfigs (#9236)
- only run easyconfigs test suite with Python 2.7 & 3.6 + Lmod 7 in Travis CI (#9297)
- archive ACML easyconfigs (#9367)
- update CMake build in Eigen 3.3.7 to use more recent toolchain (#9398)
v4.0.1 (October 15th 2019)
--------------------------
update/bugfix release
- added example easyconfig files for 58 new software packages:
- ADOL-C (#9098), ALFA (#9106), ASTRID (#9088), Annif (#8536), bnpy (#8989), bpp-core (#9064), bpp-phyl (#9064),
bpp-seq (#9064), Clang-Python-bindings (#9084), CPB (#5869), Centrifuge (#8714), Chromaprint (#9047), Con3F (#8755),
DeepSurv (#8096), Essentia (#9054), FastRFS (#9088), GAT (#5871), Gaia (#9049), Gctf (#9097), GenomeMapper (#5872),
Infomap (#9091), kpcalg (#8740), libglvnd (#9111, #9130), libsamplerate (#9046), libssh (#8865), libzip (#9073),
MetaboAnalystR (#8773), Metaxa2 (#8939), MotionCor2 (#8942), NFFT (#9085), PhyML (#9103), PlaScope (#8714),
PyCharm (#9100), pbcopper (#8928), pbmm2 (#8929), phylokit (#9088), phylonaut (#9088), phyx (#9090), pycma (#8834),
Q6 (#9069), Qt5Webkit (#9120), ROME (#9050, #9062), rioxarray (#9007), SVDquest (#9088), savvy (#9124),
sciClone (#7806), shapAAR (#8983), shrinkwrap (#9124), Structure (#5866), trimAl (#9063), thurstonianIRT (#9080),
TurboVNC (#9110, #9111, #9128), Tracer (#8970), TagLib (#9048), TRIQS (#8835), THetA (#8875), vcfnp (#5862),
WebSocket++ (#8842)
- added additional easyconfigs for various supported software packages, including:
- Armadillo 9.700.2, arpack-ng 3.7.0, BLASR 5.3.3, Bazel 0.26.1 + Bazel 0.29.1, Cufflinks 20190706,
DL_POLY_Classic 1.10, FFmpeg 4.2.1, Go 1.13.1, Horovod 0.18.1, IOR 3.2.1, Julia 1.2.0, LLVM 9.0.0, Mesa 19.1.7,
Molden 6.1, Mono 6.4.0.198, NCO 4.8.1, , Net-core 3.0.0, Nim 1.0.0, OpenFOAM 2.2.x, PGI 19.7, PLUMED 2.5.2,
PMIx 3.1.4, PostgreSQL 11.3, psycopg2 2.8.3, QGIS 3.4.12, QScintilla 2.11.2, Qt5 5.13.1, ReFrame 2.19,
Rust 1.37.0, Spack 0.12.1, TAMkin 1.2.6, TensorFlow 1.14.0 w/ fosscuda/2019a, TensorFlow 2.0.0 w/ foss/2019a,
UCX 1.6.1, VEP 96.0, xarray 0.13.0
- added easyconfigs for fosscuda/2019a toolchain (#9066)
- minor enhancements, including:
- add EBImage extension to easyconfig for R-bundle-Bioconductor 3.9 (#8982)
- add check for http:// URLs in easyconfig files added/changed in PRs (#9012)
- add bbmle/emdbook/SOAR/rasterVis/tictoc extensions to R 3.6.0 easyconfigs (#9037)
- updated PyQt5 5.12.1 easyconfig to also build sip files + minor readability changes (#9071)
- enabled SQLITE_ENABLE_COLUMN_METADATA, which is needed for GDAL (and QGIS) (#9118)
- also install include/GL/internal/ for recent Mesa installations (#9129)
- various bug fixes, including:
- add ncurses as dependency to lftp (#8646)
- add patch for gettext 0.19.8* to avoid picking up global git config that could break the installation (#8957)
- fix source_urls in GlimmerHMM easyconfigs (#8980)
- add patch for PyTorch 1.2.0 to use version of torchvision that is compatible with PyTorch 1.2.0 (#8986)
- clarify the comment regarding the optarch setting in ITK-5.0.1 (#8991)
- fix homepage & description in easyconfig file for YAPS (#8993)
- add patch for PyTorch 1.2.0 to fix failing softmax test on Intel Sandy Bridge (#9010)
- fix permissions for TRF (#9034)
- ICU needs Python 2.7+ to build, so add that as builddependency (#9053)
- fix urls for Anaconda and Miniconda (#9087)
- use a cuDNN version that has support for the CUDA version in fosscuda/2019a (CUDA 10.1) in PyTorch, TensorFlow and Theano easyconfigs (#9112)
- other changes:
- make sources in CUDA 10.1.105 use %(cudaarch)s template value (to use different source on POWER systems) (#8136)
- update Java/1.8 wrapper to Java/1.8.0_221 (#9038)
- allow divergent Java dep version as long as it's indicated by versionsuffix (#9041)
v4.0.0 (September 20th 2019)
----------------------------
feature release
- fixes due to changes in easyBuild-framework v4.0.0
- use SYSTEM toolchain + fix local variable names to fix broken tests after collapse of 4.x branch into develop (#8369, #8711, #8822)
- fix names of local variables (#8682-#8688, #8690, #8695-#8702, #8709, #8710, #8715, #8717, #8718, #8720-#8732)
- enable --local-var-naming-check=error for easyconfigs tests (#8784)
- stick to 'dummy' toolchain for now in easyconfig for latest EasyBuild 3.x (#8829)
- fix compatibility with Python 3: also run easyconfigs tests with Python 3.5, 3.6 and 3.7 (#7778, #7836, #8293)
- added easyconfigs for new common toolchains: foss/2019b (#8567), intel/2019b (#8681)
- iccifort is now installed as a single entity (no more separate icc/ifort installations from intel/2019b onwards) (see also #8879)
- versionsuffix has been stripped down for toolchain components (GCC/binutils/OpenBLAS versions are no longer included)
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added example easyconfig files for 28 new software packages:
- AGFusion (#8840), Bonmin (#8855), causalml (#8871), ClonalFrameML (#6082), Control-FREEC (#8794), corner (#8886),
CVXPY (#8662), cytosim (#8368), dill (#8885), Dsuite (#8713), GDCHART (#8679), gifsicle (#8664), guenomu (#8677),
JsonCpp (#8841), libxml++ (#8896), LOHHLA (#7227), Longshot (#8830), MDBM (#8850), nglview (#8860),
ownCloud (#6804), ptemcee (#8884), pubtcrs (#7500), pyiron (#8860), qpth (#8665), QtKeychain (#6804),
rgdal (#8826), smallgenomeutilities (#8507), umis (#8812)
- added additional easyconfigs for various supported software packages, including:
- Blosc 1.17.0, bokeh 1.3.4, cURL 7.66.0, csvkit 1.0.4, dask 2.3.0, Extrae 3.7.1, FSL 6.0.1, GLibmm 2.49.7,
git 2.23.0, IPython 7.7.0, numexpr 2.7.0, OSU-Micro-Benchmarks 5.6.2, OpenBLAS 0.3.7, OpenSSL 1.1.1d,
ParaView 5.5.2, Paraver 4.8.1, Perl 5.30.0, PnetCDF 1.10.0, Porechop 0.2.4, PyTables 3.5.2, PyTorch 1.2.0,
Python 2.7.16 + 3.7.4, parallel 20190622, phonopy 2.2.0, QIIME2 2019.7, Qiskit 0.12.0, REMORA 1.8.3,
scikit-image 0.15.0, spglib-python 1.14.1.post0, torchvision 0.3.0, X11 20190717
- various additional minor enhancements, including:
- add several extensions to R 3.6.0 easyconfigs (#8843, #8881)
- add pRoloc to R-bundle-Bioconductor v3.9 (#8882)
- clean up OpenMPI 3.1.* and 4.* easyconfigs to use custom OpenMPI easyblock (#8889, #8890)
- update numexpr easyconfigs to use custom easyblock for numexpr (#8901)
- switch to PythonBundle & enable use_pip in old dask easyconfig files (#8922)
- update CrayCCE, CrayGNU, CrayIntel and CrayPGI toolchains to 19.06 (#8944)
- various bug fixes, including:
- make TensorFlow 1.7.0 work for AMD CPUs (#6256)
- make sure that right Python wrapper is used in VTK8 (#7296)
- update the PyPI trove classifiers (#8298)
- add missing checksum for matplotlib v3.0.3 (#8643)
- add patch to plugins/Make-arch to use the correct Tcl library version in VMD (#8820)
- fix issue where 'print_qiime_config.py -t' sanity check command fails for QIIME 1.9.1 because of missing subdir in $PYTHONPATH (#8838)
- update homepage info in likwid (#8846)
- disable threading in preprocessCore extension included with Bioconductor 3.9 to work around conflict with OpenBLAS's threading (#8847)
- add -lrt patch to PyTorch 1.1.0 easyconfig (#8852)
- fix incorrect escaping in SIP configure options in PyQt5 easyconfigs (#8856)
- add missing Autotools build dep for fastq-tools (#8858)
- add missing deps for zlib, bzip2, and XZ for angsd (#8867)
- apply patch to R package uroot in R 3.6.0 (#8872)
- consider archive source URL for all extensions in R-tesseract easyconfig (#8897)
- add pkg-config build dep for tesseract v4.0.0 (#8898)
- fix source_urls in byacc easyconfig files (#8899, #8908)
- add missing cairo dependency to PRINSEQ easyconfig file (#8902)
- configure OpenMPI 1.10.x with --without-ucx to avoid problems when ucx-devel is installed in the OS (#8903)
- add GDAL 3.0.0 for Python 2.7.15 and fix the Python 3.7.2 version (#8912)
- fix homepage & description in scikit-image easyconfigs (#8916)
- add faulthandler patches to Python 3.7.0 easyconfigs (#8832)
- other changes:
- archive ancient CUDA 5.0.35 easyconfigs with creative way of determining sources (#7796)
- remove ancient easyconfigs from archive (#8542)
- archive easyconfigs using deprecated toolchains (#8557, #8558, #8585)
- archive ancient versions of GC3Pie/GCC/OpenMPI/ORCA (#8586) & CPLEX (#8765)
- rename SALMON to SALMON-TDDFT to fix name clash with Salmon (#8613)
- bump AnnotationDb version in bundle for Bioconductor 3.9 (#8854)
- stop trying to use setuptools.setup in setup.py, always use distutils.core.setup instead (#8866, #8892, #8894)
- archive easyconfigs using ancient Cray* toolchains (#8945)
v3.9.4 (August 23rd 2019)
-------------------------
update/bugfix release
- added example easyconfig files for 36 new software packages:
- ArrayFire (#8461), BRAKER (#8437), bwidget (#8477), Catch2 (#8703), core-counter (#8749), CubeGUI (#6328),
CubeLib (#6328), CubeWriter (#6328), dagitty (#8606), enaBrowserTool (#8795), GEMMA (#8270), GeneMark-ET (#8437),
GenomeThreader (#8437), ieeg-cli (#8793, #8811), Judy (#8543), Julia (#8578), libaio (#8543), libtirpc (#8792),
magick (#8545), MSM (#8556), MSPC (#8531), mygene (#8809), OpenMolcas (#7699), PhiPack (#8750), plc (#8796),
plotly.py (#8756), pymemcache (#8663), PySCF (#8736), qcint (#8736), Qiskit (#7592), QuaZIP (#8672), re2c (#8543),
SeqAn3 (#8651), snippy (#8635), spaln (#8437), V8 (#8676)
- added additional easyconfigs for various supported software packages, including:
- ASE 3.18.0, BEDTools 2.28.0, Bowtie 1.2.3, bzip2 1.0.8, CPLEX 12.9, CUDA 10.1 update 2, cyvcf2 0.11.5,
EIGENSOFT 7.2.1, GC3Pie 2.5.2, GCC(core) 9.2.0, GPAW 19.8.1, GlobalArrays 5.7, IMB 2019.3, imageio 2.5.0,
jemalloc 5.2.0, nodejs 10.15.3, PyTorch 1.1.0, pybedtools 0.8.0, Quandl 3.4.8, R 3.6.0 w/ intel/2019a,
R-bundle-Bioconductor 3.9, Salmon 0.14.1, Scalasca 2.5, Score-P 6.0, Stacks 2.41, TensorFlow 1.14.0, ToFu 1.4.0,
WIEN2k 19.1, Wannier90 3.0.0, XCrySDen 1.5.60
- minor enhancements, including:
- add patch and dependencies to easyconfig for Qt5 5.12.3 to fix Xlib support & enhance the installation (#8544)
- update nodejs to version 10.15.3 and build libnode and libv8 shared libs (#8546)
- add extensions to R 3.6.0 easyconfig: MIIVsem (#8565), medflex (#8680), Rserve/spls (#8758), Boruta/CovSel/ctmle/BayesPen (#8805)
- include PyQtWebEngine bindings in easyconfig for PyQt5 5.12.1 using Python 3.7.2 (#8572)
- switch GLX backend to Gallium in Mesa-19.0.1 (#8594)
- various bug fixes, including:
- fix typo in description in GroopM easyconfig file (#8346)
- add missing bugfix patch to easyconfig for OpenMPI 3.1.4 (#8566)
- downgrade AtomPAW to last supported version in ABINIT 8.10.3 (#8571)
- switch easyconfig for glew 2.1.0 to ConfigureMake easyblock (#8595)
- fix checksum for source tarball in foss/2018b easyconfig of NAMD v2.13 (#8602)
- update URL for bzip2 easyconfigs (#8614)
- add patch for M4 1.4.17 to fix installation on top of glibc 2.28 (#8666)
- add patch for Bison 3.0.4 to fix installation on top of glibc 2.28 (#8675)
- avoid needless requirement for matplotlib < 3.0.0 in MultiQC easyconfigs (#8691)
- fix checksum in OpenMPI 1.8.8 easyconfigs (#8692)
- add alternative checksums for nlme/mgcv/foreign/boot extensions in R 3.5.1 and 3.6.0 easyconfigs (#8564, #8762)
- add missing core-counter dependency for worker 1.6.8 (#8749)
- add missing pkg-config build dependency in various easyconfigs for (#8763, #8775, #8777, #8776, #8764, #8787, #8816)
- add patch to Python 3.7.2 easyconfig to fix faulthandler segfault (#8781)
- set $CPLUS_INCLUDE_PATH in easyconfigs for older matplotlib versions (#8785)
- patch out removed glibc 2.28 header from GCC libsanitizer (#8789)
- include sysmacros.h directly to work around removal from glibc header in numactl easyconfig (#8790)
- adapt gzip's bundled gnulib for glibc 2.28 (#8791)
- add libtirpc and depend on it in easyconfig for libdap 3.20.3 (#8792)
- add missing YAML extension to Perl 5.28.0 easyconfig (required by BioPerl scripts) (#8806)
- other changes:
- remove broken easyconfigs for ciftify due to non-trivial missing dependencies (#8560)
v3.9.3 (July 8th 2019)
----------------------
update/bugfix release
- added example easyconfig files for 25 new software packages:
- Arb (#8137), AtomPAW (#8506), ciftify (#8457), cysignals (#8459), deal.II (#8440), FastQTL (#8449), FLINT (#8137),
gdbgui (#8488), gearshifft (#8482), jbigkit (#8442), lavaan (#8539), libRmath (#8449), OR-Tools (#8364, #8523),
p4est (#8440), ppl (#8459), pplpy (#8459), PRISMS-PF (#8440), PyAPS3 (#8398), pyEGA3 (#8418), ReFrame (#8481),
S4 (#8487), SALMON (#8478), TM-align (#8510), UnZip (#8474), XTandem (#8517)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 8.10.3, CFITSIO 3.47, GDB 8.3, GROMACS 2019.3, HEALPix 3.50, HPCG 3.1, Nilearn 0.5.2, OpenBLAS 0.3.6, Xerces-C++ 3.2.0
- minor enhancements, including:
- update easyconfig for CFITSIO 3.45 with https and sanity check (#8472)
- add AtomPAW and Wannier90 support to ABINIT 8.10.2 easyconfig (#8506)
- add 'resample' extension to R 3.5.1 + 3.6.0 easyconfigs (#8538)
- various bug fixes, including:
- fix source URLs for Mesa 17.{2,3} with fosscuda toolchain (#8446)
- add in Boost dependency to canu-1.8-foss easyconfigs (#8470)
- stick to Ubuntu Trusty when testing with Python 2.6 in Travis (#8483)
- fix incorrect order of extensions for Python-2.7.14 easyconfigs (pycparser and cffi must come before cryptography) (#8495)
- suppress installation of libbfd and libopcode for GDB (#8496)
- fix KronaTools easyconfigs to make sure symlinks in bin are not broken (#8508)
- make additional configopts in PETSc easyconfigs work after uncommenting (#8522)
- add pkg-config build dep to easyconfig for pocl 1.2 (#8528)
- download correct source tarball for Net-core 2.1.8 (#8530)
- fix 'Permission denied' error when running 'cp -a' for ANTs 2.3.1 installation by first removing the .git subdirectories causing them (#8535)
- fix checksum for boot 1.3-22 extension in R 3.6.0 easyconfig (#8537)
v3.9.2 (June 9th 2019)
----------------------
update/bugfix release
- added example easyconfig files for 17 new software packages:
- adjustText (#8354), cowsay (#8380), fxtract (#8426), google-java-format (#8373), libtar (#8379), mkl-service (#8390),
msprime (#8371), pygrib (#8395), pyhdf (#8394), pyproj (#8395), PyStan (#8410), Racon (#8358), rapidtide (#8256),
SingleM (#8428), smafa (#8420), SVDetect (#8399), Unicycler (#8376)
- added additional easyconfigs for various supported software packages, including:
- BLAST+ 2.9.0, Boost.Python 1.70.0, DIAMOND 0.9.24, EMAN2 2.3, ecCodes 2.12.5, GDAL 3.0.0, ImageMagick 7.0.8-46,
Libint 2.5.0, matplotlib 2.2.4, NLopt 2.6.1, OrfM 0.7.1, PGI 19.4, PostgreSQL 11.3, R 3.6.0,
R-bundle-Bioconductor 3.8, Rust 1.35.0, STAR 2.7.1a
- minor enhancements, including:
- use CMake rather than configure script for libxc 4.3.4 (#8361, #8453)
- add 'cobs' extension to R 3.5.1 easyconfigs (#8389)
- add sanity check command to PSI4 1.2.1 easyconfigs to ensure that 'import psi4' works (#8393)
- include the provided backports patch in QuantumESPRESSO-6.4.1 (#8405)
- add Logger::Simple, Scalar::Util::Numeric, YAML, Object::InsideOut extensions to Perl 5.28.1 easyconfig (#8432)
- update Java 1.8 to 1.8.0_212 (#8443)
- various bug fixes, including:
- add missing builddep on gettext to ATK/2.28.1 for fosscuda/2018b (#8402)
- add patch to fix OpenBLAS v0.3.1 matrices multiplication issue (#8396)
- make Eigen a build dependency for nanopolish (#8448)
- other changes:
- clean up ELPA 2018.11.001 easyconfig to use custom easyblock for ELPA (#8360)
- remove unused checksum for ballgown extension in Bioconductor 3.7 easyconfigs (#8363)
v3.9.1 (May 20th 2019)
----------------------
update/bugfix release
- added easyconfigs for new toolchains:
- fosscuda/2019a (#8063), gimkl/2018b (#8287), gomkl/2018b (#8216), gomkl/2019a (#8218), intelcuda/2019a (#8069)
- added example easyconfig files for 52 new software packages:
- ADDA (#8207), AMD-LibM (#7164), AMD-RNG (#7165), AMD-SecureRNG (#7165), ARGoS (#8039, #8104), ARWEN (#8213),
Canvas (#7716), cdsapi (#7970), charmm (#8202), emcee (#7989), FlexiDot (#8228, #8275), FreeImage (#8039),
Hello (#7704), HLAminer (8094), hypothesis (#8307), imgaug (#8229), INTEGRATE (#8193, #8304), INTEGRATE-Neo (#8094),
IRkernel (#8050, #8099), JiTCODE (#7148, #8327), libFLAME (#7163), libpsml (#5859), LibSoup (#8116),
libutempter (#6426), LS-PrePost (#8070), LUSCUS (#7191, #8105, #8285), memory-profiler (#8255), metaWRAP (#7896),
Net-core (#7716), netMHC (#8094), Nextflow (#8195), nvtop (#8024), openpyxl (#8121), py-cpuinfo (#8245),
pyFFTW (#8198), PyQtGraph (#7525, #8253), R-tesseract (#7933), RBFOpt (#8178), rnaQUAST (#8040), RStan (#7996),
scikit-multilearn (#8142), simpy (#8177, #8250), SMARTdenovo (#7630), socat (#8305), SymEngine (#7148, #8327),
unixODBC (#8074), VAtools (#7938), VirtualGL (#8008), WebKitGTK+ (#8118, #8241), xmlf90 (#5858), YAPS (#7976),
zingeR (#7264)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.70.0, cairo 1.16.0, CGAL 4.14, Clang 8.0, cutadapt 2.1, dask 1.1.4, ELPA 2018.11.001, FFmpeg 4.1.3,
GCC 9.1.0, GEOS 3.7.2, GLib 2.60.1, gmsh 4.2.2, GROMACS 2019.2, GTK+ 3.24.8, h5py 2.9.0, hwloc 1.11.12,
Hypre 2.15.1, Mathematica 12.0.0, matplotlib 3.0.3, Mesa 19.0.1, NBO 7.0, NCL 6.6.2, NCO 4.7.9,
NiBabel 2.4.0, numba 0.43.1, OpenMPI 3.1.4, OrthoFinder 2.3.3, PCMSolver 1.2.3, PETSc 3.11.1,
PROJ 6.0.0, PyQt5 5.12.1, PyTorch 1.0.1, PyYAML 5.1, Qt5 5.12.3, QuantumESPRESSO 6.4.1, R 3.5.1 (w/ intel/2018b),
RNAIndel 1.0.0, Ruby 2.6.3, scikit-learn 0.20.3, SLEPc 3.11.0, sympy 1.4, Tkinter 3.7.2, Vim 8.1.1209, VTK 8.2.0,
wrf-python 1.3.1, wxPython 4.0.4, wxWidgets 3.0.4, xarray 0.12.1, zstd 1.4.0
- minor enhancements, including:
- enable auto-download of VMD 1.9.3 + add patches for Surf and Stride (#7305)
- add mlegp extension in R 3.5.1 easyconfigs (#7814)
- add pkg-config file to bzip2 easyconfigs (#8200)
- allow use of 'use_pip = False' in easyconfigs if pip doesn't work (#8220)
- various bug fixes, including:
- fix checksums for nlme extensions in R easyconfigs (#7814, #8054)
- add missing XZ dependency for Pysam > 0.12 (#7971)
- define $GRACE_HOME in Grace easyconfigs, so that font dir can be located (#8048)
- $XDG_DATA_DIRS must be set for GTK+ (#8089)
- add missing FriBidi dependency for Pango 1.43.0 (#8103)
- add (back) custom sanity_check_paths in recent Pango easyconfigs (#8106)
- fix missing extensions in cutadapt 1.16 easyconfigs (#8130)
- add missing cURL dependency for recent SAMtools versions (#8131)
- add singledispatch extension to Python 2.7.15 easyconfig using GCCcore/8.2.0 toolchain (#8164)
- add missing X11 dependency for Gdk-Pixbuf 2.38.1 (#8222)
- make sure hdf5r picks up HDF5 dependency in R 3.5.1 easyconfigs (#8223)
- enable zstd compression in GRASS 7.6.0 easyconfig (#8224)
- add missing ICU dependency on ICU for Harfbuzz 2.4.0 (#8226)
- disable AVX512 DGEMM kernels in OpenBLAS 0.3.5 (#8227)
- fix homepage/description in OrthoFinder easyconfig (#8234)
- add Parallel::ForkManager extension to Perl 5.28.x easyconfigs (#8247)
- replace LibUUID dependencies with util-linux (#8258)
- add jemalloc & pkg-config as build deps for Salmon 0.12.0 (#8264)
- fix MAJIQ easyconfig by fixing order of extensions + avoid numpy test hang (#8272)
- fix shebang in GLib Python script + clarify runtime dependency on Python (#8277)
- add `pkg-config` and `expat` as (build) dependency for DBus (#8283)
- define $GI_TYPELIB_PATH in GTK+ and Pango easyconfigs (#8246, #8286)
- add pkg-config build dep to PROJ/6.0.0 (#8309)
- fix source URLS in recent libcerf easyconfigs (#8332, #8243)
- make zlib a real dependency rather than a build dep in recent binutils easyconfigs (>= 2.28) (#8340)
- add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs (#8341)
- set $XDG_CACHE_HOME to $TMPDIR before 'pip install' in Arrow 0.12.0 easyconfigs (#8347)
- other changes:
- remove xbitmaps dependency from motif (#7530)
- require custom sanity_check_paths in easyconfigs touched in PRs when generic easyblock is used (#8101, #8123)
- use CMake built with GCCcore toolchain when installing Eigen 3.3.4+ (#8261)
- fix Python classifiers in setup.py, should be (only) Python 2.6 & 2.7 (#8299)
- use custom easyblock for OpenBLAS in OpenBLAS 0.3.x easyconfigs (#8345, #8339)
v3.9.0 (April 12th 2019)
------------------------
feature release
- added easyconfigs for new toolchains: intel/2019.02 (#7598), intel/2019.03 (#7846)
- added example easyconfig files for 68 new software packages:
- ACT (#7928), aiohttp (#7728), at-spi2-atk and at-spi2-core (#7658), Bader (#7804), barrnap (#7738), BCEL (#7937),
biscuit (#5868), bitarray (#7772), BlobTools (#7565, #7583), bmtagger (#7890), bsddb3 (#7642),
CheckM (#7712), Cheetah (#7952), CONCOCT (#7891), cyvcf2 (#8031), DAS_Tool (#7741), ExaBayes (#7801),
FastANI (#7992), fastp (#7693), Flask (#7734), giflib (#7663), Giza (#7843), glew (#7685), gpustat (#8025),
GRASS (#7489), GTDB-Tk (#7995), HPCX (#7725), IntelPython (#7920), KNIME (#7554), KronaTools (#7721),
KyotoCabinet (#7955), Leptonica (#7932), libepoxy (#7655), libpsl (#7666), MAGMA (#7829), MATLAB-Engine (#7758),
MaxBin (#7767), MetaBAT (#7746, #7931), MinPath (#7763), ncdu (#7505), NGSadmix (#7524), NIMBLE (#7564),
PCAngsd (#7727), pizzly (#7724), Ploticus (#7545), pocl (#7681), POT (#8011), ProjectQ (#7576), pullseq (#7740),
pyBigWig (#7600), Pyke3 (#8034), PyRETIS (#8041), RDKit (#7973), RNAIndel (#8009), scikit-optimize (#7613),
SciPy-bundle (#7922), sep (#8032), slidingwindow (#7909), SPLASH (#7843), SqueezeMeta (#7771), SRPRISM (#7890),
taxator-tk (#7894), TensorRT (#7584), tesseract (#7932), Transrate (#5108), VCF-kit (#7786, #7882), VV (#7297)
- added additional easyconfigs for various supported software packages, including:
- AFNI 19.0.01, Arrow 0.7.1, BLAST+ 2.8.1, CUDA 10.1.105, GCC(core) 8.3.0, GTK+ 3.22.30, Java (OpenJDK) 11(.0.2),
Meson 0.50.0, MultiQC 1.7, Nim 0.19.2, Ninja 1.9.0, netCDF 4.6.2, netCDF-Fortran 4.4.5, PCRE 8.43, Perl 5.28.1,
PGI 19.1, Python 3.7.2, RELION 3.0.4, Ruby 2.6.1, SCons 3.0.4, SQLite 3.27.2, SuiteSparse 5.4.0, TINKER 8.6.1,
TensorFlow 1.13.1, X11 20190311
- minor enhancements, including:
- add various extensions to R 3.5.1 easyconfigs: asnipe (#7572), liquidSVM (#7597), oddsratio/mltools/h2o (#7744),
mlegp (#7814), bartMachine/lqa (#7865), PresenceAbsence/GUTS/GenSA (#7905), parsedate (#7935), circular (#7975)
- add ujson extension in recent Python easyconfigs (#7517)
- run various checks on easyconfigs that are touched in pull requests and involve Python packages (#7754)
- add cpanminus extension to recent Perl easyconfigs (#7866)
- also install ANTs scripts (and set $ANTSPATH as required by those scripts) (#7940)
- add missing configopts in GATE 8.1 easyconfig to enable Davis feature (#8000)
- various bug fixes, including:
- add patch for Mesa 18.1.1 to detect MIT-SHM (#7536)
- add proper description to MINC-2.4.03 (#7551)
- add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (#7629)
- add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs (#7696)
- fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) (#7743)
- use https in most recent XZ easyconfigs (#7782)
- add patch for OpenMPI 3.1.x to fix ib-query 'Invalid argument' error (#7789)
- build OpenBLAS with -fno-tree-vectorize (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (#7790, #7793)
- extra patch for TensorFlow 1.12.0 to remove -B/usr/bin from linker_bin_path_flag in cuda_configure.bzl (#7800)
- fix easyconfig for STAR-Fusion 1.5.0 (#7802)
- fix checksums for boot/nlme extensions in R easyconfigs (#7814, #8054)
- add patch for OpenMPI 3.x to fix UCX memory leak (#7535, #7824)
- replace ncurses-devel OS dependency in CMake easyconfigs using dummy toolchain with proper ncurses dependency (#7834)
- use PythonBundle for snakemake-5.2.4-foss-2018b-Python-3.6.6.eb (+ fix moduleclass) (#7842)
- use correct buildopts + add missing zlib dependency in StringTie 1.3.5 easyconfig (#7845)
- update GStreamer to not enable dw and fix some missing dependencies (#7889)
- add missing XZ dependency to most recent Pysam easyconfigs (#7897)
- expat: add configure option --without-docbook to avoid docbook2X dependency (#7930)
- fix source URLs for mawk (#7960)
- fix LWM2, OTF2, OPARI2, and Score-P download URLs (#7994)
- use https:// in homepage & source_urls for OpenMPI and hwloc easyconfigs (#8013, #8014, #8015 and #8016)
- add missing bokeh dependency for dask 1.0.0 (+ add dask-jobqueue) (#8029)
- fix checking of binutils build dep in easyconfig tests (#8038)
- other changes:
- avoid use of .items() in R (bundle) easyconfigs, to fix compatibility with EasyBuild running on top of Python 3 (#7791)
- trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (#7795, #7798)
- use %(pyshortver)s template in (old) SIP easyconfigs (#7797)
- add PyTorch to whitelist for not having 'use_pip' enabled (#7844)
- don't use local variable 'pylibdir' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 (#7848)
- use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains (#7864)
- prefer https:// over ftp:// for source_urls in recent GROMACS easyconfigs (#7948)
- rename arrow to Arrow for old easyconfig (#8007)
v3.8.1 (January 29th 2019)
--------------------------
bugfix/update release
- added easyconfigs for new toolchains foss/2019a (#7371), intel/2019a (#7372) and iomkl/2019.01 (#7375)
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added example easyconfig files for 43 new software packages:
- Assimulo (#6740), C3D (#7059), CellMix (#7422), CESM-deps (#6654, #6675, #6823), DSA (#7422),
DeMixT (#7422), deconf (#7422), DeconICA (#7422), double-conversion (#7307), dxpy (#7079), EPIC (#7422),
expect (#7387), Flye (#7430), FMILibrary (#6740), FMRIprep (#7059), FUSE (#7078), GDCM (#7310), HDDM (#7396),
ICA-AROMA (#7059), IntaRNA (#7334), imageio (#6738), KWIML (#7308), kWIP (#7444), MagresPython (#7395), medaka (#7426),
MINC (#7311), MuSiC (#7422), netMHCIIpan (#7377), NIfTI (#7311), OPERA (#7408), psrecord (#7331), pyfits (#7273),
PyFMI (#6740), PyGWAS (#5852), Pylint (#6675), QDD (#7284), RERconverge (#7289), samclip (#7226), SCIPhI (#7419),
swarm (#7453), VXL (#7309), wrf-python (#6736), xCell (#7422)
- added additional easyconfigs for various supported software packages, including:
- Amber 18, Arrow 0.12.0, Biopython 1.73, Boost 1.69.0, CP2K 6.1, canu 1.8, Ferret 7.3, GATE 8.1.p01, GROMACS 2019,
Geant4 10.5, HPL 2.3, libxsmm 1.10, matplotlib 3.0.2, NEURON 7.6.5, Octave 4.4.1, OpenBLAS 0.3.5, OpenCV 3.4.5 + 4.0.1,
OpenFOAM v1812, PGI 18.10, PLUMED 2.5.0, ROOT 6.14.06, Theano 1.0.3, TopHat 2.1.2, Yade 2018.02b
- minor enhancements, including:
- add additional extensions to R 3.5.1 easyconfigs:
- statnet (#7370), NMF, ComICS, dtangle, MCMCpack, shinythemes (#7420), csSAM (#7423), bridgedist (#7477)
- add DeconRNASeq and GSVA extensions to R-bundle-Bioconductor 3.7 easyconfigs (#7421)
- also install header files and CMake module for SeqAn 2.4.0 built with foss/2018b (#7434)
- add download URL for intel/2018a components (#7436)
- add missing checksums for protobuf easyconfigs using dummy toolchain (#7492)
- various bug fixes, including:
- fix source URL in Doxygen easyconfigs (#7324)
- add fallback source URL for recent pigz versions (#7346)
- promote FriBiDi to runtime dep of Pango rather than only build dep (#7369)
- add --without-systemdsystemunitdir configure option to recent DBus easyconfigs (#7373)
- fix issue of building M4 1.4.18 with glibc 2.28 (#7384)
- fix broken source URLs in MariaDB easyconfigs (#7413)
- bump up build dependency of flex 2.6.4 from Bison 3.0.4 to 3.0.5 (#7414)
- disable building of OpenColorIO Python bindings since Python is not included as a dependency (#7416)
- add missing build dependencies in old Harfbuzz/Pango easyconfigs (2016a generation) (#7433)
- fix XML-LibXML linking with Intel compiler and GCCcore Perl (#7440)
- prevent non-critical error from stopping Guile v1.8.8 build (#7446)
- use %(arch)s template rather than hardcoding 'x86_64' in XML-Parser easyconfigs (#7450)
- use uniform configopts for Guile 1.8.8 (#7452)
- fix configopts in PyQt5 easyconfig files to avoid installation of files in Python/Qt5 installation directories (#7470)
- other changes:
- fix homepage in easyconfigs for 'foss' toolchains (#7482) and 'intel' toolchains (#7483)
v3.8.0 (December 14th 2018)
---------------------------
feature release
- added easyconfigs for new toolchains: intel/2018.04 (#7171), intel/2019.00 (#7218), intel/2019.01 (#7219)
- added example easyconfig files for 36 new software packages:
- 4ti2 (#7040), ARPACK++ (#6750), CellRanger (#7242), CharLS (#6762) cscope (#7057), ctags (#7057), datamash (#6693),
dcm2niix (#6762), DCMTK (#6761), deepdiff (#7109), Drake (#7182), fast5 (#7250), gap (#7040), Gerris (#7211),
GPAW-setups (#6984), iCount (#7080), ipyparallel (#6797), Kratos (#7149), LCov (#7160), libvdwxc (#6984),
libwebp (#7065), lrslib (#7040), MuPeXI (#6991), netMHCpan (#6991), Normaliz (#7040), OpenColorIO (#7146),
OpenJPEG (#7216), PHLAT (#7036), poppler (#7069), RECON (#7042), RepeatMasker (#7281), TreeMix (#7133),
unrar (#7117), utf8proc (#7083), VSEARCH (#7153), XMDS2 (#7121)
- added additional easyconfigs for various supported software packages, including:
- CheMPS2 1.8.8, Clang 6.0.1 + 7.0.0, dask 1.0.0, FFmpeg 4.1, GCC(core) 6.5.0 + 7.4.0, GPAW 1.4.0, HMMER 3.2.1,
IPython 7.2.0, ITK 4.13.1, Keras 2.2.4, LLVM 7.0.0, Mothur 1.41.0, MultiQC 1.6, NAMD 2.13, OpenBLAS 0.3.4,
OpenMPI 3.1.3 + 4.0.0, PSI4 1.2.1, Qt5 5.11.2, QuantumESPRESSO 6.3, Rust 1.30.1, Spark 2.4.0, Spyder 3.3.1,
TensorFlow 1.11.0 + 1.12.0
- minor enhancements, including:
- install misc tools for angsd (#6995)
- add libXp component to X11 bundle for GCCcore 6.4.0 (#7062)
- also install shared libraries for LZO (#7073)
- add extensions to R 3.5.1 easyconfigs: gllvm (#7123), grpreg (#7140), gamlss + gamlss.tr (#7263)
- install Tk private headers (#7155)
- add File::Next extension to Perl 5.28.0 easyconfig (#7276)
- various bug fixes, including:
- fix installation of scikit-image 0.13.x by including missing required PyWavelets extension (#7061)
- add missing dependencies to easyconfig for GC3Pie 2.5.0 (#7066)
- stop setting ignored 'full_sanity_check' easyconfig parameter in easyconfigs (#7094)
- add missing checksums in X11/2016* easyconfigs (#7095)
- add missing checksums in X11/2017* easyconfigs (#7096)
- add missing cffi & pycparser extensions to recent Python easyconfigs (#7105, #7118)
- fix homepage in QuantumESPRESSO easyconfigs (#7114)
- use empty toolchain version in picard easyconfigs to ensure Java dependency is loaded during installation (#7116)
- fix checksum for mgcv extension in R 3.5.* easyconfigs (#7122)
- add missing 'patsy' extension in ARCH easyconfig + switch to using PythonBundle easyblock (#7124)
- add missing (dummy) sklearn extension in NeuroKit easyconfig (#7126)
- fix order of extensions in recent IPython easyconfigs to make 'pip check' pass (#7131)
- fix missing required Python packages in ASE 3.16.2 easyconfigs (#7139)
- fix source_urls in CP2K easyconfigs (for official releases) (#7240)
- update SCOTCH 6.0.5 easyconfigs in-place to 6.0.6 to fix wrong download URL (#7159)
- add Autotools build dep in patchelf easyconfig (#7175)
- STREAM fixes: use https + versioned source (#7193)
- fix checksum in Molden easyconfig (#7251)
- fix source URL for ADMIXTURE (#7258)
- fix source URLs & versions + build procedure for SKESA (#7275)
- fix checksum for TRF 4.09 (#7278)
- add missing zlib dependency for NSS (#7293)
- add required build deps for QtWebEngine in recent Qt5 easyconfigs (#7300)
- fix ImageMagick source URLs: use launchpad.net for old versions, switch to GitHub for 7.0.8-* onwards (#7301)
- other changes:
- update Java/1.8 wrapper to Java 1.8.0_192 (#7097)
- don't enable optarch toolchain option in VCFtools easyconfigs, since it's enabled by default (#7106)
- stop using lowopt in libxc 4.2.3 easyconfigs (#7115)
- deprecate easyconfigs for ictce toolchains + intel toolchains older than intel/2016a (#7231)
- deprecate easyconfigs for goolf(c) + corresponding gompi(c) subtoolchains (#7243)
v3.7.1 (October 18th 2018)
--------------------------
bugfix/update release
- added easyconfigs for new toolchain foss/2018.08 with GCC/8.2.0 (#6992)
- added example easyconfig files for 26 new software packages:
- ARCH (#6939), fbm (#6948), GenomeTester4 (#6970), GlobusConnectPersonal (#6974), MMseqs2 (#6964), NAG (#5772),
NAGfor (#5772), NSPR (#7005), NSS (#7005), NeuroKit (#6947), novoalign (#6944), OptiType (#6924),
OrthoFinder (#6964), pandas-datareader (#6938), pFUnit (#6949), PMIx (#6930), PSolver (#6888), PyDatastream (#6951),
PyFR (#6846), Pyomo (#6910), Quandl (#6950), RTG-Tools (#6862), seq2HLA (#6969), suds (#6951), UCX (#6931), XMLSec (#6929)
- added additional easyconfigs for various supported software packages, including:
- binutils 2.31.1, dask 0.19.4, GCC(core) 8.2.0, OpenBLAS 0.3.3, OpenMPI 3.1.2, Pillow 5.3.0, PyCUDA 2018.1
- minor enhancements, including:
- add clustree + plotly extensions (+ deps) for R 3.5.1 (#6901)
- add tclsh symlink to recent Tcl easyconfigs (#6915)
- update GROMACS 2016.3 with NVML patches (#6936)
- use make=make in build options for ParMGridGen easyconfigs (#6952)
- add Data::Dump as extension to Perl (dependency for GIMIC) (#7004)
- various bug fixes, including:
- inhibit -Werror in binutils 2.26 as new system GCC has case fallthrough warnings (#5793)
- change fastStructure easyconfig to use custom easyblock (#6893)
- fix toolchain for tbb dependency in Bowtie2-2.3.4.2-foss-2018b.eb (#6927)
- fix uroot installation in R-3.5.1-foss-2018b (#6934)
- add missing Python packages in TensorFlow 1.10.x easyconfigs (#6940)
- add missing dep for Szip in 2017b builds of netCDF (#6942)
- fix missing comment from OpenBabel-2.4.1-fix-link-path-tests.patch (#6943)
- add patch to Python 3.6.1 - 3.6.3 that removes comment in comment (#6946)
- add missing ulimit_unlimited=True (see issue #6484) in the newest Python builds (#6959)
- solve 'version UUID_1.0 not found' problem in LibUUID easyconfigs (#6962)
- eliminate dependency on ancient problematic LibUUID library, replace with util-linux (#6963)
- force building of ccmake for CMake 3.12.1 + fix deps (#6967)
- fix broken installation for Python 3.6.2 & 3.6.3 with PyNaCl as dep for paramiko extension by explicitely including previous PyNaCl version as extension (#6971)
- fix source URL for ADMIXTURE (no https) + add SHA256 checksum (#6982)
- add missing NSS/DBus dependencies to Qt 5.10.1 easyconfigs built with foss toolchain to ensure that QtWebEngine component gets installed (#7005)
- add 'openssl' OS deps in Perl 5.28.0 easyconfig for Net::ssleay (#7008)
- add missing checksum for ipaddress extension in Python easyconfigs (#7021 and #7033)
- add missing extensions to Python 2.7.14 (#7022 and #7023), 3.6.2 (#7025), 3.6.3 (#7027) and 3.6.4 (#7029 and #7030)
- add missing OS dependencies for git (#7028)
- create default configuration for RTG-Tools (#7032)
- also run checks on changed files when target branch for PR is something different than 'develop' (#7034)
- other changes:
- removed dead 'bzip.org' source URL for bzip2 source tarball (#6983)
v3.7.0 (September 25th 2018)
----------------------------
feature release
- added easyconfigs for new toolchains: fosscuda/2017b (#6706), intelcuda/2017b (#6709), iomkl/2018b (#6661)
- added example easyconfig files for 49 new software packages:
- alleleCount (#6676), BCALM (#6796), BDBag (#6672), BFC (#6647), Bio-DB-HTS (#6854), bioawk (#6865),
biomart-perl (#6745), BLIS (#6614), Boost.Python (#6763), BWISE (#6802), CapnProto (#6542), CaVEMan (#6708),
CCL (#5802), cDNA_Cupcake (#6787), cget (#6780), coevol (#6589, #6642), Delly (#6735), earthengine-api (#6556),
fineRADstructure (#6586), GIMIC (#6575), GitPython (#6850), HiC-Pro (#5873), Inelastica (#6831), JAXFrontCE (#6837),
jq (#6632), KAT (#6808), KMC (#6553), Kraken2 (#6569), Lighter (#6553), Mash (#6542), MetaPhlAn2 (#6600),
Minimac4 (#6781), mordecai (#6670), NCCL (#5802), NxTrim (#6646), parasail (#6601), PheWAS (#6030), Pilon (#6553),
python-parasail (#6601), SearchGUI (#6637), shovill (#6553), SKESA (#6553), snakemake (#6851), strelka (#6742),
SWIPE (#6795), ToFu (#6322), tqdm (#6721), TRUST (#6601), VEP (#6854)
- added additional easyconfigs for various supported software packages, including:
- Bazel 0.16.0, Boost 1.67.0 + 1.68.0, CUDA 10.0.1, DOLFIN (FEniCS) 2018.1, FSL 5.0.11, GC3Pie 2.5.0, GROMACS 2018.3,
HTSlib + SAMtools 1.9, IPython 6.4.0, matplotlib 3.0.0, OpenCoarrays 2.2.0, OpenFOAM 6 & v1806, PyTorch 0.4.1,
Python 3.6.6, R 3.5.1, TensorFlow 1.10.1, Trilinos 12.12.1, WIEN2k 18.1
- minor enhancements, including:
- add test to enforce SHA256 checksums in touched files in pull requests to develop (#5005)
- add various extensions to recent R easyconfigs (#6590, #6686, #6858)
- add mpmath extension to Python 3.6.4 + 3.7.0 easyconfigs (#6607, #6713)
- add Java 1.8 easyconfig that can be updated in-place to more recent JDK 1.8.x (#6712)
- see also https://easybuild.readthedocs.io/en/latest/Wrapping_dependencies.html
- add iso_c_binding support to arpack-ng 3.6.2 (#6718)
- add XML::Parser XML::RegExp XML::DOM extensions to Perl(#6744)
- add tabulate extension to all Python > 3.6 easyconfigs (#6809)
- enable MPI version of arpack-ng 3.5.0 (#6840)
- add wish -> wish8.6 symlink to Tk (#6870)
- add libXp and printproto to X11 bundle (#6873)
- various bug fixes, including:
- define '_GNU_SOURCE' to ensure that 'reallocarray' is defined in flex 2.6.4 easyconfigs, fixes bootstrap crash (#5792, #6766)
- added tabix dependency in VCFtools (#6584)
- added zlib dependency to BWA (#6591), BEDTools (#6592), VCFtools (#6653)
- add checksums to googletest easyconfigs (#6611)
- fix source URL + add checksum to wkhtmltopdf-0.12.3-Linux-x86_64.eb (#6628, #6641)
- don't use external FoX dependency in QuantumESPRESSO 6.2 (#6638)
- update hwloc easyconfigs with libxml2 and libpciaccess dependencies (#6639)
- fix gettext build dep for Mono-5.10.0.160 (#6640)
- remove no longer existing config option --enable-mpi-thread-multiple in OpenMPI 3.x easyconfigs (#6645)
- fix homepage in recent HDF5 easyconfigs (#6687)
- add expat dependency to Mesa v18.1.1 (#6706)
- add missing --with-trio-flavor=netcdf flag to ABINIT 8.x easyconfigs (#6711)
- remove useless definition of $TORCH_CUDA_ARCH_LIST in PyTorch easyconfig that doesn't use CUDA (#6719)
- fix builing GCCcore 6.3.0 on recent OSs by backporting patches from 6.4.0 (#6727)
- fix source_urls in bzip2 easyconfigs (#6728)
- specify location of dependencies in configure options for libgd (to avoid system libraries being used instead) (#6731)
- also install docs/man pages in recent git easyconfigs (versions 2.1x.y) (#6751)
- add CMake build dep for Eigen 3.3.4 (#6756, #6784)
- add expat dependency to Perl 5.26.0 (#6758)
- add ncurses OS dependency to CMake for Debian distros (#6783)
- fix checksums for pkgmaker, rngtools & RcppProgress extensions in R 3.4.3 easyconfigs (#6815)
- add pkg-config build dependency to GTS (#6819)
- do not check if hwloc-dump-hwdata utility was installed, since it's only built on x86 systems (#6836)
- patch libxc 3.x and 4.0.x to compile on POWER (#6868)
- consistently add patch for paycheck extension in Python 3.6/3.7 to fix UTF8 issue with README (#6892)
- other changes:
- bump Lmod version used in Travis config to 6.6.3 (now required by framework) (#6834)
v3.6.2 (July 11th 2018)
-----------------------
bugfix/update release
- added easyconfigs for new toolchains: foss/2018b (#6424), fosscuda/2018b (#6555) and intel/2018b (#6409)
- added example easyconfig files for 28 new software packages:
- CUnit (#6469), eggnog-mapper (#6513), FANN (#6468), FTGL (#6421), FreeFem++ (#5918), fastStructure (#6448),
fastq-tools (#5396), fullrmc (#6422), GDGraph (#6529), heaptrack (#6450), libgpuarray (#5429), lz4 (#6449),
MAJIQ (#5983), makedepf90 (#6504), nanopolish (#6464), opencv_contrib (#6441), PRC (#6477), Pillow-SIMD (#6152),
Pytorch (#6152), poretools (#6467), pystran (#6395), R-keras (#6530), Scoary (#6521), Scrappie (#6469),
torchvision (#6152), WISExome (#6524), WannierTools (#6539), zstd (#6449, #6452)
- added additional easyconfigs for various supported software packages, including:
- GROMACS 2018.2, HDF5 1.10.2, IPython 6.3.1, Kraken 1.0, Mesa 18.1.1, netCDF 4.6.1, NWChem 6.8, OpenBLAS 0.3.1,
OpenMPI 3.1.1, Perl 5.28.0, Python 2.7.15, R 3.5.0, X11 20180604
- minor enhancements, including:
- add hint on file name differences between downloaded and expected in cuDNN easyconfig (#6042)
- add 'gee' extension to R 3.4.4 easyconfigs (#6376)
- enable building of MPI libraries in VTK 8.1.0 easyconfigs (#6460, #6429)
- minor changes, including:
- rename 'Canu' to 'canu' for v1.7 (#6389)
- update existing easyconfigs for OpenCV 3.4.1 to use new custom easyblock for OpenCV (#6509)
- fix software name in Bsoft easyconfig (#6557)
- various bug fixes, including:
- fix SAMtools dependency for ChimPipe, required SAMtools < 1.0 (#5930)
- skip installing of documentation in easyconfig for jemalloc 5.0.1 (#6428)
- stop including GCCcore 6.4.0 as build dep for GCCcore 8.1.0 (#6431)
- no longer needed with updated GCC easyblock
- add patch for GCCcore 6.4.0 to fix compilation problems on glibc 2.26 systems (#6432, #6495)
- fix checksums for pkgmaker/rngtools/RWeka/RcppProgress/mgcv extensions in R 3.4.4 easyconfigs (#6446, #6502)
- added necessary compiler flag for Guile 1.8.8 (#6457)
- build hwloc 1.11.10 with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake (#6461)
- add patch for binutils 2.30 to fix assertion failure (#6463)
- sync extensions in Python-3.6.4-iomkl-2018a.eb easyconfig with other Python 3.6.4 easyconfigs using 2018a toolchain (#6471)
- enable checking/setting of unlimited stack limit in Python 3.6.x easyconfigs using an 'intel' toolchain (#6485, #6492)
- add missing libxml2 dependency for HDF5 1.10.1 (#6498)
- also copy eggnog-mapper scripts (#6522)
- fix missing dependencies for Perl modules included as extensions for Perl 5.26.1 (#6532) and 5.28.0 (#6533)
- fix location of include directory in libffi 3.2.1 easyconfigs (#6565)