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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 8,479 easyconfig files, for 1,725 different software packages,
incl. 31 different (compiler) toolchains.
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)
- other changes
- also check for multiple dependency variants in easyconfigs using GCCcore 7.3.0 & newer (#6444)
v3.6.1 (May 28th 2018)
----------------------
bugfix/update release
- added easyconfigs for new toolchains fosscuda/2018a (#6363) and giolfc/2017b (#5799)
- added example easyconfig files for 24 new software packages:
- BAGEL (#6332), Bottleneck (#6334), cisTEM (#6370), cftime (#6337), dotNET-Core-Runtime (#6345), ecCodes (#6235),
feh (#6300), Graphene (#5043), gffread (#6306), HOME (#6227), HiCExplorer (#6342), ICU (#6371), Imlib2 (#6300),
KmerGenie (#5929), libgeotiff (#6262), NetPIPE (#6062), Pandoc (#6247), Pisces (#6347), Proteinortho (#6333),
pyshp (#6364), SIMPLE (#6019), STIR (#6349), SimpleElastix (#6114), wxWidgets (#6370)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.67.0, ESMF 7.1.0r, GATK 4.0.4.0, GCC 8.1.0, GROMACS 2018, OpenBLAS 0.3.0, PETSc 3.9.1, PGI 18.4,
TensorFlow 1.8.0, WIEN2k 17.1
- minor enhancements, including:
- add py_expression_eval extension to (recent) Python 2.7.14 & 3.6.4 easyconfigs (#6285)
- add README for Java with information on downloading source tarball (#6294)
- add several extensions to Perl 5.26.1 easyconfigs, incl Dist::Zilla & dependencies (#6297)
- also include archive URLs for Bioconductor 3.6 (#6311)
- add README.md file for installing icc/ifort (#6317)
- various bug fixes, including:
- consistently specify 'intel-mkl' component in recent Intel MKL easyconfigs (#6234)
- add pkg-config as build dependency to libdrm (#6243)
- add pkg-config build dep to most recent libdrm easyconfigs (#6244)
- fix checksum for foreign extension in R 3.4.3 and R 3.4.4 easyconfigs (#6245)
- fix installation of Libint 2.4.2 by building with -std=c++11 (#6251)
- fix source spec for networkx 2.1 extension in scikit-image easyconfig (#6254)
- avoid that Nipype downloads dependencies for included extensions (#6261, #6263)
- consistently include patch for FLTK 1.3.4 (#6265)
- fix Perl shebang in MCL v14.137 scripts (#6269)
- add patch to build particular source file of matrixStats extension in R 3.4.4 easyconfig with -O1 to work around ICE in Skylake systems (#6278)
- add pkg-config build dependency to FFmpeg >= 3.3.1 (#6291)
- change back checksum for libdap 3.19.1 (#6305)
- add patch for Automake 1.15 to fix issue with recent Perl versions (#6358)
- fix ``glog`` causing intel error in Intel compilers on Intel Skylake (#6360)
- include ICU as dependency in recent R easyconfigs (v3.4.3 & v3.4.4) (#6371)
- fix checksum for RSEM 1.3.0 after sneaky re-release (#6379)
v3.6.0 (April 26th 2018)
------------------------
feature release
- added easyconfigs for new toolchain golf/2018a (#6080)
- added example easyconfig files for 39 new software packages:
- ARAGORN (#6138, #6219), amask (#6105), BamBam (#5490), Bandage (#6053), bcgTree (#6057), biobambam2 (#6040),
CODEX2 (#5972), coverage (#5964), DANPOS2 (#5870), EasyQC (#6175), elastix (#6074), FRANz (#6035), Filtlong (#6050),
FriBidi (#6181), Gblocks (#6057), Grace (#6036), LMfit (#6119), libmaus2 (#6040), MathGL (#6033),
MiGEC (#6047), MiXCR (#6045), Miniconda3 (#6075), Multiwfn (#5403), mosdepth (#6169), Nim (#6167),
Porechop (#6051), propy (#6091), Roary (#6056), Rtree (#6222), SALib (#6145), SMRT-Link (#6218), SimpleITK (#6172),
spectral.methods (#6104), supernova (#6193), TEToolkit (#5912), tbl2asn (#6139), udocker (#5770), vartools (#6102),
XCfun (#5975)
- added new easyconfigs for existing toolchains:
- gmpich/2017.08 (#6143), goolfc/2018a (#6129), intel/2018.02 (#6077), iomkl/2018.02 (#6088)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 8.6.3, Anaconda2 5.1.0, Anaconda3 5.1.0, binutils 2.30, dask 0.17.2, FFmpeg 4.0, GCC(core) 7.3.0
GROMACS 2016.5, olf 2018a.eb, HTSlib 1.8, LLVM 6.0.0, Mesa 17.3.6, netCDF 4.6.0, Octave 4.2.2, OpenCV 3.4.1,
PLUMED 2.4.1, PROJ 5.0.0, PostgreSQL 10.3, Qt5 5.10.1, R 3.4.4, SAMtools 1.8, Spack 0.11.2 TensorFlow 1.7.0,
VTK 8.1.0
- minor enhancements, including:
- add test to ensure there's only one variant for each dependency in dep graph of easyconfigs using particular toolchains (#5970, #6023)
- add extensions required by CODEX2 v20180227 to Bioconductor w/ R 3.4.3 (#5972)
- add config file for https://pre-commit.com/ (#5785)
- add custom sanity check paths for GraphicsMagick consistently (#5997)
- add custom sanity check paths to recent Ghostscript easyconfigs (#5998)
- add svd, Rssa, JBTools, RUnit, DistributionUtils and gapfill extensions for R 3.4.3 (#6099)
- add additional extensions to Bioconductor 3.6 bundle (#6136)
- add xlrd extension to recent Python 2.x and 3.x easyconfigs (#6162)
- minor changes, including:
- use gettext 0.19.8.1 on top of libxml2 2.9.7 as dep for git built with foss/2018a (#5993)
- bump hwloc dep for OpenMPI 2.1.2 that is part of iomkl/2018a to v1.11.8 (#5994)
- use non-interactive plotting backend by default for matplotlib 2.1.2 (#6024)
- don't use bare Perl as dependency for git with foss/2018a, use variant with extensions (#6058)
- various bug fixes, including:
- fix moduleclass & add custom sanity_check_paths in gettext easyconfigs (#5991)
- drop use of --disable-dlopen in (recent) OpenMPI easyconfigs due to negative performance impact (#6060)
- add missing XZ dep in Python 3.6.4 easyconfigs built with */2018a toolchain (#6065)
- add 10 packages that were previously downloaded in Python 3.6.4 easyconfigs (#6081)
- add patch for Tensorflow 1.6 & 1.7 to include missing -lrt link flag (needed in CentOS6) (#6089)
- fix checksums for R extensions that were updated in place in easyconfigs for R versions 3.4.3 & 3.4.4 (#6118)
- include pkg-config as build dep in recent R easyconfigs (required for atleast nloptr) (#6122)
- remove Intel-specific workaround for 'undefined symbol: __stack_chk_guard' issue from Python 3.6.4 foss/2018a easyconfig (#6130)
- add configopt --without-matlab/octave to all NLopt easyconfigs (#6132)
- also consider lib64 in sanity_check_paths for Bison 3.0.4 (#6170)
- don't use libyaml built with dummy as dep for PyYAML (#6208)
- add missing pkg-config build dep in recent GObject-Introspection, GLib & cairo easyconfigs (#6216)
- don't include (ancient version of) Time::HiRes as Perl extension, since it's a core Perl module (#6225)
- this fixes problems with the installation of BioPerl and proovread
- add missing XML-LibXML dependency in recent BioPerl easyconfigs (#6226)
- add --without-ada configure option in recent ncurses easyconfigs (#6228)
- add patch for snaphu to fix segmentation fault due to use of short integer (#6230)
v3.5.3 (March 7th 2018)
-----------------------
bugfix/update release
- added example easyconfig files for 2 new software packages:
- CNVkit and hmmlearn (#5954)
- added additional easyconfigs for various supported software packages, including:
- matplotlib 2.1.2, TensorFlow 1.6.0
- minor enhancements, including:
- re-enable testing against environment modules, bump Lmod to 7.7.16 (#5944)
- add cghFLasso extension to R 3.4.3 easyconfigs (#5953)
- add 'Math::CDF' extension to recent Perl modules (#5957)
- various bug fixes, including:
- add missing --enable-ld-version-script configure option for LibTIFF 4.0.9 built with GCCcore/6.4.0 (#5945)
- hard disable UCX support in recent OpenMPI versions, to dance around bug in OpenMPI configure script (#5949)
v3.5.2 (March 2nd 2018)
-----------------------
bugfix/update release
- added example easyconfig files for 24 new software packages:
- AMPL-MP (#5800), AmberTools (#5632), bcolz (#5864), detonate (#5709), dropEst (#5734), EvidentialGene (#5627),
faceswap (#5825), fineSTRUCTURE (#5663), Gradle (#5828), gbs2ploidy (#5877), HIPS (#5725), Ipopt (#5800),
libMemcached (#5804), MEGAHIT (#5748), Mmg (#5807), methylpy (#5874), pstoedit (#5884), python-igraph (#5905),
RNAcode (#5854), Seq-Gen (#5695), Stata (#5102), scikit-allel (#5864), TetGen (#5681), zarr (#5864)
- added new easyconfigs for existing toolchains: giolf/2018a (#5777), goolfc/2017b (#5768), iomkl/2018a (#5878)
- added additional easyconfigs for various supported software packages, including:
- CP2K 5.1, IPython 6.2.1, OpenFOAM v1712, Perl 5.26.1, Python 3.6.4, TensorFlow 1.5.0, X11 20180131
- minor enhancements, including:
- add feather and tidyverse as extensions for R 3.4.3 (#5693)
- build recent PLUMED versions with all modules enabled (#5696)
- add MAST/splatter/scDD to Bioconductor 3.6 bundle (#5704)
- add dummies as extensions for R 3.4.3 + monocle/scde/ROTS (+ deps) to Bioconductor 3.6 bundle (#5724)
- include io and statistics extensions to Octave 4.2.1 easyconfigs (#5798)
- switch to using TensorFlow as backend for recent versions of Keras (#5821)
- various bug fixes, including:
- using the correct binutils in jemalloc 5.0.1 easyconfig using GCCcore/6.4.0 (#5659)
- fix source URLs for MPC (#5662)
- add Tkinter as dependency for ASE & matplotlib using Python 3.6.3 (#5658)
- fix versions for updated extensions in Bioconductor 3.6 bundle (#5704, #5724, #5880)
- fix missing M4 build dependency in nettle (#5722)
- fix homepage for OpenFOAM 4.x & 5.x, should be openfoam.org (#5422, #5780)
- add matplotlib, cairo & PyCairo dependencies for graph-tool 2.26 + enhance sanity check (#5787)
- fix hardcoded version in scikit-image easyconfigs (#5822)
- fix pkgconfig moduleclass, 'data' doesn't make much sense (#5817)
- add sanity check in recent matplotlib easyconfigs to ensure that Tkinter is available (#5689, #5896)
- correct MPI path when building ABINIT with 'foss' toolchain (#5760)
- patch Hyperopt to make it work with networkx 2.0 (#5642)
- add Tkinter sanity check to ASE easyconfigs (#5691, #5909)
- include autotools as build dep in git easyconfigs (#5718)
- fix sanity check paths for Debian OS in JasPer easyconfigs (#5897)
- fix source_urls for recent versions of ABINIT (#5908)
- add patch for recent GDAL easyconfigs using intel toolchain to fix icc get stuck on compiling ceos.c (#5915)
- add explicit zlib dependency in Tkinter 2.x and 3.x (#5797, #5926)
- fix source URLs & homepage in Singularity easyconfigs (#5927)
- fix installation of TensorFlow 1.3 via binary wheel after introducing TensorFlow easyblock (#5938)
v3.5.1 (January 16th 2018)
--------------------------
bugfix/update release
- added easyconfigs for foss/2018a and intel/2018a common toolchains (#5577), (#5578)
- added example easyconfig files for 26 new software packages:
- BeautifulSoup (#5601), Calendrical (#5588), ChimPipe (#5560), crb-blast (#5124)), dammit (#5125), deepTools (#5536),
FastQ_Screen (#5404), FoX (#5496), GffCompare (#5581), GlimmerHMM (#5559), LocARNA (#5548), MapSplice (#5566),
MariaDB-connector-c (#5557), NextGenMap (#5430), nd2reader (#5545), PIMS (#5545), Pysolar (#5585), phono3py (#5551),
preseq (#5569), proovread (#5513), QUAST (#5610), RNA-SeQC (#5589), RNAclust (#5607), Ragout (#5608),
SOAPfuse (#5417), TransDecoder (#5125)
- added additional easyconfigs for various supported software packages, including:
- BLAST+ 2.7.1, BamTools 2.5.0, Boost 1.66.0, Clang 5.0.0, dask 0.16.0, FFmpeg 3.4.1, GROMACS 2016.4, HDF5 1.8.20,
matplotlib 2.1.1, PLUMED 2.4.0, Pillow 5.0.0, Qt5 5.9.3, QuantumESPRESSO 6.2, Ruby 2.5.0, Rust 1.22.1
- minor enhancements, including:
- include gomms in list of extensions for R 3.4.3 (#5547)
- clean up BamTools easyconfigs to rely on updated easyblock + add SHA256 checksums (#5575)
- add Time::HiRes to recent Perl versions (#5616)
- add DNAcopy & dupRadar extensions to bundle for Bioconductor 3.6 (#5587, #5618)
- switch to using install_target rather than now deprecated use_easy_install and use_setup_py_develop (#5625)
- various bug fixes, including:
- avoid auto-downloading of parcel in gdc-client 1.3.0 easyconfig (#5523)
- fix permissions on make_raw_alos.pl script in ROI_PAC installation (#5546)
- remove erroneous patch for Intel compiler support in Perl 5.26.0 easyconfig built with GCCcore/6.4.0 (#5561)
- include HWxtest as extension to fix issue with diveRsity in R 3.4.3 easyconfig file (#5570)
- add pkg-config as build dependency for fontconfig, harfbuzz, gnuplot, pango (#5580)
- fix versions of updated extensions in BioConductor bundle (#5587, #5618)
- add missing libpng dependency in ROOT 6.10.08 easyconfigs (#5595)
- fix option passed to configure in M4 (#5606)
- rename SIBELia to Sibelia (#5603)
- add patch for binutils 2.26 to fix compatibility with GCC 6.x (#5611)
- fix for dependencies was set twice in OpenMPI 3.0.0 easyconfig (#5619)
- fix download URL in comment of Kent tools easyconfigs (#5633)
- add SHA256 checksums to various easyconfigs (#5635, #5636, #5639)
- add rdma-core-devel to OS dependencies for OpenMPI 3.0.0 (#5648)
v3.5.0 (December 15th 2017)
---------------------------
feature release
- added example easyconfig files for 39 new software packages:
- AmberMini (#5476), arrow (#5416), bat (#5416), CIRCexplorer (#5356), CIRCexplorer2 (#5470), CIRI (#5358),
FALCON (#5265), FastaIndex (#5465), find_circ (#5348), future (#5236), GapCloser (#5465), glibc (#5428),
GRNBoost (#5373), HDFView (#5391), Horovod (#5239), HPDBSCAN (#5371), Hyperopt (#5455), IntelClusterChecker (#4970),
ITK (#5434), LAST (#5465), MDTraj (#5317), Meson (#5228), mkl-dnn (#5319, #5362), Ninja (#5228), OpenKIM-API (#5479),
ParmEd (#5476), PCRaster (#5386), piSvM (#5308), piSvM-JSC (#5316), PTESFinder (#5359), pybedtools (#5347),
pymbar (#5476), pyScaf (#5465), QIIME2 (#5355), QTLtools (#5361), Redundans (#5465), Rmath (#5361), sbt (#5373),
SNAP (#5465)
- added new easyconfigs for existing toolchains: intel/2017.09 (#5303), intel/2018.00 (#5129), intel/2018.01 (#5345)
- added additional easyconfigs for various supported software packages, including:
CGAL 4.11, CMake 3.10.0, Caffe 1.0, FFTW 3.3.7, GATE 8.0, gnuplot 5.2.2, HPCG 3.0, HTSlib 1.6, Keras 2.1.2,
LLVM 5.0.0, Mesa 17.2.5, mpi4py 3.0.0, netCDF 4.5.0, OpenFOAM 5.0, ParaView 5.4.1, R 3.4.3, Ruby 2.4.2, Rust 1.21.0,
SCons 3.0.1, Szip 2.1.1, Theano 1.0.0, VTK 8.0.1, X11 20171023
- minor enhancements, including:
- add SHA256 checksums to Autoconf (#5304), Automake (#5305), libtool (#5306) and M4 (#5307) easyconfigs
- avoid hardcoding extension versions in worker easyconfig, include 'perl' as OS dep (#5324)
- enable building ScaLAPACK in parallel with enhanced ScaLAPACK easyblock (#5331)
- include RInside extension in R 3.4.0 easyconfig (#5354)
- clean up configure options that are now handled by R easyblock (#5478, #5485)
- update Octave easyconfigs to use Octave easyblock, add extensions for latest Octave versions (#5484, #5503, #5507)
- add Log4perl extension to Perl 5.26.0 easyconfigs (#5511)
- various bug fixes, including:
- add missing extensions required by MultiQC & stick to networkx 1.11 (#5240)
- disable optarch when using intel compilers and enable tests in all libxc easyconfigs (#5256, #5257)
- avoid downloads when installing matplotlib 2.1.0 w/ Python 2.7.14 (#5267)
- fix $CPATH in recent libffi easyconfigs + enhance sanity check & add checksum (#5271)
- use Github source URL, run autogen.sh + include Autotools build dep for numactl (#5286, #5296, #5297, #5299, #5302)
- add hwloc to GROMACS dependencies (#5295)
- fix source_urls (& sources spec) for GATE (#5367)
- consistently add Autotools build dep in recent netCDF easyconfigs (#5394)
- fix check in test suite for binutils build dep when GCCcore used as toolchain (#5436)
- libdap 3.19.1 checksum changed (#5473)
- disable new rfkill feature in easyconfig for util-linux 2.31 since it requires a recent kernel (#5480)
- add missing PROJ dependency in recent GDAL easyconfigs (#5481)
- fix name in TensorFlow easyconfigs (was 'TensorFlow') (#5495)
- fix checksum for Szip 2.1.1 (#5517)
- fix order of extensions for FSLeyes, add missing MarkupSafe (dep for Jinja2) (#5520)
v3.4.1 (October 17th 2017)
--------------------------
bugfix/update release
- added easyconfigs for new toolchain giolf/2017b (#5140)
- added example easyconfig files for 13 new software packages:
- ASAP3 (#5200), Albacore (#5153), CatMAP (#5225), DLCpar (#5209), FSLeyes (#5192), IQ-TREE (#3695), NEST (#5515),
nanonet (#5149), OMA (#5211), oxford_asl (#5193), QEMU (#5220), REMORA (#5159), SAS (#5208), supermagic (#5187)
- added additional easyconfigs for various supported software packages, including:
- Anaconda2/3 4.4.0, Blender 2.79, Boost 1.65.1, CMake 3.9.4, FFmpeg 3.3.4, GCC 5.5.0, h5py 2.7.1, Keras 2.0.8,
matplotlib 2.1.0, mympingpong 0.8.0, OpenCV 3.3.0, OpenFOAM-Extend 4.0, OpenMPI 2.1.2 + 3.0.0, Pillow 4.3.0,
Python 2.7.14 + 3.6.2, SAMtools 1.6, scikit-image 0.13.0, scikit-learn 0.19.0, Tensorflow 1.3.0, vsc-mympirun 4.0.2
- minor enhancements, including:
- add xkeyboard-config component in X11 bundle (#5066)
- clean up use of wcleanAll in OpenFOAM-Extend easyconfigs, now handled by OpenFOAM easyblock (#5131)
- also install run_rcorrector.pl with Rcorrector (#5135)
- add SHA256 checksum to PyCUDA easyconfig (#5154)
- fix/improve description in HDF5 easyconfigs (#5182)
- include heatmap3 extension for R 3.4.0 (#5185)
- add ComplexHeatmap to Bioconductor 3.5 bundle + dep pkgs in R 3.4.0 easyconfig (#5195)
- various bug fixes, including:
- fix source URLs for AUGUSTUS 3.2.3 (#5119)
- fix building Bison 2.5 on systems with recent glibc (#5130)
- also consider rdma-core-devel as alternative to libibverbs-devel OS dependency (#5132)
- consistently use empty toolchain version in icc & ifort easyconfigs to ensure that GCC(core) dep is loaded during installation (#5133, #5134)
- add patches for Boost 1.64.0 to fix known issues (#5148)
- remove PyCUDA easyconfig for intel/2017a, doesn't work due to incompatibility between GCC 6.3.0 & CUDA 8 (#5156)
- add missing Perl extensions in easyconfig for Worker 1.6.7 (#5157)
- fix checksums for packages that download from ``github.com/x/y/archive`` (#5162)
- add missing libpng dependency to g2lib-1.4.0 easyconfig using intel-2017a (#5196)
- fix source_urls for Szip 2.1 & include SHA256 checksum (#5206)
- remove unneeded --with-fft-incs configure option for ABINIT (#5207)
- disable optarch for libjpeg-turbo 1.5.1 built with intel/2017a (#5214)
- update $R_LIBS in plotly easyconfig (#5215)
- include NLopt as a dependency in R easyconfigs that include nloptr as extension (#5217)
v3.4.0 (September 10th 2017)
----------------------------
feature release
- added easyconfigs for foss/2017b and intel/2017b common toolchains (#4768), (#4618)
- added new easyconfigs for existing toolchains:
- iomkl/2017b (#5097)
- added example easyconfig files for 31 new software packages:
- BAMM (#4650), BamM (#4650), bcl2fastq2 (#4902), CGNS (#5078), CLAPACK (#5096), CLISP (#4926, #4986),
cadaver (#4873), destiny (#5009), GroopM (#4650), Lucene-Geo-Gazetteer (#5064), libffcall (#4850),
libsigsegv (#4840), MERCKX (#5056), minimap2 (#4991), ncompress (#4852), OpenNLP (#5059, #5061),
OpenRefine (#5058), PHAST (#5096), PYTHIA (#5083), ParallelIO (#5071), PnetCDF (#5071), plotly (#5010),
QML (#5101), Quorum (#5095), Rcorrector (#5095), SCnorm (#5008), SOAPdenovo-Trans (#5095), Shannon (#5095),
Tika (#5063), UNAFold (#4997), VERSE (#4843)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1,
MRtrix 3.0_RC2, Perl 5.26.0, ROOT 6.10.04, Spark 2.2.0
- minor enhancements, including:
- add checksums to Perl 5.24.1 easyconfigs (#4973, #4992)
- add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (#5007, #5028, #5029, #5062, #5079)
- also define $INCLUDEPATH and $LIBRARY_PATH in Tesla-Deployment-Kit easyconfig (#5018)
- add check to see whether binutils is included as build dep when GCCcore toolchain is used (#5084)
- various bug fixes, including:
- added Rmpi patch file for R built with intel toolchains incl. impi 5.x (#4623)
- use single-line description in setup.py (#4881)
- fix version and source for Seurat + add extensions required by Seurat in R 3.4.0 easyconfig (#4889)
- add zlib as dependency to util-linux easyconfigs (#4900, #4998)
- use modextrapaths instead of modextravars in OpenMM easyconfig (#4903)
- update deprecated PLINK urls (#4920, #5006)
- fix moduleclass for Cookiecutter (#4947)
- fix order of OpenMPI dependency in iomkl easyconfig, must come after icc/ifort (#5024)
- fix typo in comment in util-linux easyconfigs & add SHA256 checksums (#5052)
- remove superfluous $CPATH update in GLib 2.44.0 easyconfig (#5053)
- update ncurses to not build a separate libtinfo but provide a soft link instead + force linking to ncurses in libreadline (#5067, #5074)
- include Autotools as build dep for netCDF (#5077)
- add missing binutils build dep for texinfo (#5099)
v3.3.1 (July 12th 2017)
-----------------------
bugfix/update release
- added example easyconfig files for 6 new software packages:
- FastME (#4811), geopy (#4821), Miniconda2 (#4841), ngmlr (#4818), OpenCoarrays (#4799), Seurat (#4832)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, numpy 1.13.0, Tensorflow 1.2.0
- minor enhancements, including:
- add SVG and Statistics::Basic to recent Perl versions (#4796)
- remove buildopts from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (#4779)
- include joblib as extension in recent Python easyconfigs (#4805)
- changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (#4807)
- get rid of references to 'hpcugent' organisation after move to github.com/easybuilders (#4815, #4837)
- add Rtsne as extension to R 3.4.0 (#4831)
- various bug fixes, including:
- use PYPI_SOURCE as source URL in Tensorflow easyconfigs (#4786)
- fix homepage for skewer (#4791)
- sync/fix source_urls & homepage in HDF5 easyconfig (#4800)
- fix ubsan error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 with system GCC 7.1 (#4813)
v3.3.0 (June 26th 2017)
-----------------------
feature release
- enable automatic style checks in easyconfig tests (#2506)
- added example easyconfig files for 28 new software packages:
- ada (#4594), Aspera-CLI (#4635), AUGUSTUS (#4624), ada (#4594), Bio-SamTools (#4637), Bpipe (#4590), BUSCO (#4624),
CNVnator (#4649), davix (#4755), EricScript (#4594), FUNWAVE-TVD (#4743), gmpy2 (#4609), gSOAP (#4755),
libsndfile (#4628), lpsolve (#4264), LUMPY (#4682), MaSuRCA (#4706), modred (#4729), MXNet (#4765),
NRGLjubljana (#4651), OrfM (#4703), Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603),
sharutils (#4745), Spyder (#4627), Tkinter (#4620), VariantMetaCaller (#4632)
- added new easyconfigs for existing toolchains:
- gimkl/2017a (#4646)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1
- minor enhancements, including:
- use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files (#4606, #4619)
- add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ libsndfile as dep) (#4628, #4680, #4747)
- also copy README for GapFiller (#4631)
- enable inclusion of version symbol by using --enable-ld-version-script configure option for LibTIFF (#4639)
- add SHA256 checksums for libpciaccess to discriminate from old tarballs that required running autogen.sh (#4688)
- fix NE_GLOBAL_DIR path for ne by also specifying PREFIX in buildopts (#4698)
- more (trivial) style fixes (#4761)
- avoid use of import in ANSYS & MATLAB easyconfigs (#4762)
- set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763)
- avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764)
- add the docopt module to all Python 2017a easyconfigs (#4770)
- stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (#4774)
- various bug fixes, including:
- fix typo in statsmodels source url (/sources/ -> /source/) (#4612)
- add location to DotLib.pm to $PERL5LIB for SSPACE_Basic (#4638)
- add missing /gnu/ ins ftpmirror.gnu.org source_urls, or use GNU_SOURCE where possible (#4653)
- consistently use --with-harfbuzz=no configure option in freetype easyconfigs (#4668)
- use --with-x=yes in R easyconfigs that include X11 as a dependency (#4701)
- remove '4.0' in tbb description (#4707)
- add lib sanity check paths for Debian compatibility in nettle (#4722)
- fix source URLs for HDF5 (#4749)
v3.2.1 (May 12th 2017)
----------------------
bugfix/update release
- added example easyconfig files for 12 new software packages:
- AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544),
NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556)
- added new easyconfigs for existing toolchains:
- goolfc 2017.01 (#4577)
- added additional easyconfigs for various supported software packages, including:
- HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0
- minor enhancements, including:
- update source URLs in libpciaccess easyconfigs (#3960)
- enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555)
v3.2.0 (May 5th 2017)
---------------------
feature release
- added example easyconfig files for 34 new software packages:
- ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484),