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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 7,566 easyconfig files, for 1,293 different software packages,
25 different (compiler) toolchains, 13 software bundles and 1 meta-package.
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),
DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450),
imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), Node-RED (#4542),
PyCUDA (#4523), pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395),
rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454),
samblaster (#4435), VMD (#4391), WRF-Fire (#4403)
- added additional easyconfigs for various supported software packages, including:
- BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0,
PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5
- various enhancements, including:
- sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380)
- use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529)
- various bug fixes, including:
- add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369)
- use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384)
- fix pkgconfig patch for Qhull (#4451)
- also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467)
- add dependency NLopt for R extension nloptr (#4481)
- fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504)
- change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505)
- fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531)
- also build IMB-IO in IMB 4.1 easyconfig using foss/2016a (#4539)
v3.1.2 (March 20th 2017)
------------------------
bugfix/update release
- add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (#4334)
- note that this warrants rebuilding FFTW that is a part of foss/2017a
- added example easyconfig files for 14 new software packages:
- DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335),
L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307, #4332), QJson (#4305),
QScintilla (#4306, #4313), sketchmap (#4360), snaphu (#4362)
- added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4
- various enhancements, including:
- fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318)
- various bug fixes, including:
- correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331)
- correct libjpeg turbo references in GDAL (#4276)
- make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278)
- fix issues with miRDeep2 installation (#4291, #4301, #4316)
- also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315)
- fix PostgreSQL homepage + minor style fixes (#4318)
- detect use of '$root', which is not compatible with module files in Lua syntax (#4330)
- fix homepage/source_urls for ViennaRNA (#4338)
- pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341)
- remove include/GL/wglext.h from Mesa sanity check (#4354)
- rename S.A.G.E. to SAGE, can't have directories with trailing dot in Windows (#4368)
v3.1.1 (March 7th 2017)
-----------------------
bugfix/update release
- added example easyconfig files for 16 new software packages:
- Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175),
meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246),
Smoldyn (#4110), SpiecEasi (#4215), stress (#4180)
- added additional easyconfigs for various supported software packages, including:
- binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0,
PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a
- added new easyconfigs for existing toolchains:
- iomkl/2017a (#4216), intel/2017.02 (#4248)
- various enhancements, including:
- fix style in several easyconfigs (#4174, #4176, #4190, #4233)
- add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193)
- add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221)
- various bug fixes, including:
- add Bison and gettext as build deps for X11 (#4111)
- clean up dependencies in libdrm (#4113)
- make sure Ghostscript picks up external libraries (#4118)
- fix ippicv source download and library install for OpenCV v3.1.0 (#4126)
- fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4134, #4135)
- get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146)
- remove duplicate sources specification in OpenMPI (#4150)
- fix definition of buildopts/installopts in Cantera easyconfig (#4133, #4164, #4177)
- use http rather than ftp source URLs in CFITSIO easyconfigs (#4167)
- add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179)
- add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192)
- set CMAKE_PREFIX_PATH to ncurses install directory in CMake easyconfigs (#4196)
- switch to lowopt=True for libxc v2.2.* and v3.* (#4199)
- remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200)
- fix version (& homepage) in ea-utils easyconfigs (#4205)
- remove --with-threads configure option in OpenMPI-2.* (#4213)
- fix check for Szip library in configure script for netCDF 4.1.3 (#4226)
- fix source_urls in several easyconfigs, including:
- bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227)
v3.1.0 (February 3rd 2017)
--------------------------
feature release
- added easyconfigs for foss/2017a and intel/2017a common toolchains (#3968, #3969)
- added example easyconfig files for 16 new software packages:
- ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216),
ImageJ (#4023, #4062), libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007),
NetLogo (#3941), QIIME (#3868), QwtPolar (#4019), Tensorflow (#4084, #4095)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11
- various enhancements, including:
- update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (#3985)
- add FME extensions (+ deps) in R 3.3.1 easyconfigs (#4063)
- various bug fixes, including:
- add libxml2 dependency on HDF5 (#3759)
- remove unnecessary dependency in libmatheval (#3988)
- fix permissions on SWASH binaries (#4003)
- add conda-forge channel to perl-app-cpanminus (#4012)
- add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (#4032)
- modloadmsg style fixes in multiple easyconfigs (#4035)
- include X11 as dep for Molden (#4082)
- remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (#4083)
- fix source URLs for several easyconfigs, including:
- arpack-ng 3.1.3 + 3.1.5 (#4050), ChIP-Seq 1.5-1 (#4050), Ghostscript 9.10, 9.14 + 9.16 (#4050),
Git 1.7.12, 1.8.2 + 1.8.3.1 (#4050), HBase 1.0.2 (#4043), libevent 2.0.22 (#4037), libsodium 1.0.3 (#4046),
lynx 2.8.7 (#4050), Maven 3.2.2 and 3.3.3 (#4039), MEME 4.8.0 (#4050), PCC 20131024 (#4044), S-Lang 2.3.0 (#4045),
Spark 1.3.0 (#4041), splitRef 0.0.2 (#4040)
v3.0.2 (December 22nd 2016)
---------------------------
bugfix release
- added example easyconfig files for 13 new software packages:
- CryptoMiniSat (#3952), MATSim (#3902), Molcas (#2084), ne (#3376), psmc (#3910), PyCogent (#3897),
PyNAST (#3897), RASPA2 (#3903, #3946), SimPEG (#3876), SolexaQA++ (#3892), taco (#3882),
UCLUST (#3896), USPEX (#3767)
- added additional easyconfigs for various supported software packages, including:
- Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02
- various enhancements, including:
- trivial style fixes (#3878, #3893, #3895)
- various bug fixes, including:
- add X11 develop libs to ncview easyconfig (#3881)
- fix source_urls in pkg-config easyconfigs (#3907)
- install numpy/scipy as .egg to ensure shadowing of numpy/scipy in parent Python installation (#3921)
- fix broken source URL + homepage for Infernal (#3928)
- fix test that verifies dumped easyconfig, take into account that dumped dependencies may include hardcoded dependency (#3932)
- include libGLU as dependency in freeglut easyconfigs with recent Mesa (#3936)
- add patch for FreeSurfer to fix issue with MATLAB 2013 (#3954)
v3.0.1 (November 30th 2016)
---------------------------
bugfix release
- added example easyconfig files for 7 new software packages:
- Cookiecutter (#3827), ETE (#3857), findhap (#3860), graphviz (Python bindings, #3826), LoFreq (#3856),
PhyloBayes-MPI (#3859), XGBoost (#3849)
- added additional easyconfigs for various supported software packages
- various enhancements, including:
- add ipywidgets and widgetsnbextension extensions to IPython 5.1.0 easyconfigs (#3818, #3823)
- run dadi test suite as a sanity check command (#3858)
- various bug fixes, including:
- fix incorrect descriptions for ifort (#3817)
- fix modulename for Jinja2 and Pygments (#3823)
- fix download URL in BLAST 2.2.26 easyconfig (#3861)
v3.0.0 (November 16th 2016)
---------------------------
feature release
- backwards incompatible changes:
- archive easyconfigs using old inactive toolchains
- see #3725, #3728, #3729, #3730, #3731, #3732, #3733, #3735, #3736, #3737, #3738
- only taken into account by EasyBuild if --consider-archived-easyconfigs is enabled
- no easyconfigs available outside of archive for QLogicMPI + 15 toolchains:
- ClangGCC, cgmpich, cgmpolf, cgmvapich2, cgmvolf, cgompi, cgoolf, gmacml,
goalf, gpsmpi, gpsolf, iiqmpi, intel-para, ipsmpi, iqacml
- fix name in PyTables easyconfigs (was pyTables) (#3785)
- added example easyconfig files for 32 new software packages:
- 3to2 (#3655), Anaconda2 (#3337), Anaconda3 (#3337), ART (#3724), atools (#3631),
awscli (#3645), behave (#3751), Blosc (#3785), bokeh (#3790), Cantera (#3655),
Cargo (#3764), dadi v1.7.0, distributed (#3786), ea-utils (#3634), Elk (#3644),
FGSL (#3638), gencore_variant_detection (#3337), help2man (#3768), lbzip2 (#3791),
Log-Log4perl (#3574), Minimac2 (#3783), mypy (#3694), OBITools (#3573),
perl-app-cpanminus (#3337), PGDSpider (#3625), prokka (#3755), Reads2snp (#3609),
spglib-python (#3620), SUNDIALS (#3654, #3655), SelEstim (#3626), XMLStarlet (#3797),
x265 (#3090)
- added easyconfigs for new 'intelcuda' toolchain (#3750)
- added new easyconfigs for existing toolchains:
- goolfc/2016.08 (#3796), goolfc/2016.10 (#3666, #3775), intel/2017.00 (#3543), intel/2017.01 (#3757),
iomkl/2016.09-GCC-4.9.3-2.25 (#3680), iomkl/2016.09-GCC-5.4.0-2.26 (#3772)
- added additional easyconfigs for various supported software packages, including:
- Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3,
OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1
- various other enhancements, including:
- STREAM builds using ~56GiB and ~111GiB (#3670)
- various bug fixes, including:
- fix source spec in VASP easyconfig, ensure static linking with Intel MKL (#3381)
- fix source URL in GCCcore 6.2.0 easyconfig (#3608)
- correct STAMP dependency in i-cisTarget, must be 1.3 (#3613)
- consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#3623)
- fix source URLs for Cython (#3636)
- add Bison as build dep and M4 as runtime dep for flex 2.6.0 (#3656)
- enable parallel building of flex 2.6.0 (#3630)
- add zlib and bzip2 dependencies to X11 bundle (#3662)
- use 'letter_dir_for' function rather than just grabbing 1st letter of software name in easyconfigs tests (#3664)
- add patch to fix typo in GRIT 2.0.5 (#3675)
- fix typo in patch for WRF 3.8.0 (#3702)
- use $CC,$CXX rather than $I_MPI_CC,$I_MPI_CXX in patch for OpenFOAM 4.0 (#3703)
- patch FLTK to fix 'undefined symbol' issue when building Octave (#3704)
- include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (#3723)
- update Travis config w.r.t. changes framework config defaults and required Lmod version (#3773)
- don't limit parallellism to 4 in recent GCC easyconfigs (#3776, #3777, #3778)
- include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (#3782)
- consistently apply patch for ncurses 6.0 (#3792)
- eliminate dependency on mpi-mic-rt in ifort (#3793)
- include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (#3794)
- make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (#3795)
- include original download URL for ISL source tarball in GCC easyconfigs (#3798)
- disable installing libiberty for binutils built with intel toolchain (#3802)
v2.9.0 (September 23rd 2016)
----------------------------
feature release
- added example easyconfig files for 88 new software packages:
ADMIXTURE (#3359), angsd (#3593), ASHS (#3429), AutoDock (#3465), AutoGrid (#3466), BayeScan (#2748, #3356),
BayPass (#3451), Bazel (#3379), Blender (#3553, #3558), bwakit (#3567), BXH_XCEDE_TOOLS (#3410), CastXML (#3403),
CHASE (#3304), configparser (#3368, #3424), configurable-http-proxy (#3380), cppcheck (#3508), CRPropa (#779),
DicomBrowser (#3432), DMTCP (#3422), entrypoints (#3368, #3424), f90cache (#3570), fastPHASE (#3343),
fastQValidator (#3192), FFindex (#1135), FragGeneScan (#1198), gdc-client (#3399), gflags (#3417), glog (#3417),
GRIT (#3561), H5hut (#3431), HAPGEN2 (#3344), HEALPix (#779), IMOD (#1187, #3347), IronPython (#607),
jhbuild (#3476), jupyterhub (#3380), Keras (#3581), khmer (#1158), LeadIT (#3345, #3599), LevelDB (#3417),
libbitmask (#3481), libcpuset (#3481), LMDB (#3417), log4cplus (#1136), MACH (#3346), Mako (#3460), Maq (#3428),
MetaGeneAnnotator (#3307), Metal (#3324), Mono (#607), MyMediaLite (#607), nco (#2575), nose-parameterized (#3579),
OpenEXR (#3553), OpenImageIO (#3553), path.py (#3368, #3424), PCRE2 (#3325), pftoolsV3 (#3317), PHASE (#3385),
PLAST (#3288), PLINKSEQ (#3402), POV-Ray (#3551), ProbABEL (#3108), prompt-toolkit (#3368, #3424),
protobuf-python (#3563), PSORTb (#3317), py (#3403, #3482), pygccxml (#3403, #3482), pyGIMLi (#3403, #3482),
pyplusplus (#3403, #3482), PyQt5 (#3533), Pyro4 (#3527), pytest (#3403, #3482), QCA (#3595), RDMC (#1137),
S.A.G.E. (#3427), SDL2 (#3551), SHORE (#3531), SimVascular (#3555), SortMeRNA (#3326), SUMACLUST (#3316),
SUMATRA (#3316), Text-CSV (#3323), Triangle (#3403), VEGAS (#3457), VirSorter (#3307), wcwidth (#3368, #3424),
X11 (#3340)
- added new easyconfigs for existing toolchains:
- CrayGNU + CrayIntel 2016.06 (#3377)
- foss 2016.07 (#3517) + 2016.09 (#3523),
- iomkl 2016.07 (#3458)
- pomkl 2016.09 (#3516)
- added additional easyconfigs for various supported software packages, including:
FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0,
OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0,
Yade 2016.06a
- various enhancements, including:
- adjust PSI4 easyconfigs for updated easyblock (#3312)
- clean up libxml2 easyconfigs according to updated libxml2 easyblock (#3479, #3509)
- significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (#3520)
- include sanity checks for all MATIO config files (#3528)
- remove --with-tcl-config/--with-tk-config from R easyconfig, already done in R easyblock (#3580)
- various bug fixes, including:
- disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (#3178)
- add SQLite as dep to GDAL 2.1.0 easyconfigs (#3342)
- add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (#3342)
- add bzip2 as a dependency of freetype (#3464)
- specify correct MPI target in FDS easyconfigs (#3488)
- add tcsh as OS dep in NAMD easyconfigs (#3491)
- statically link ncurses/libreadline in Lua easyconfig with 'dummy' toolchain (#3545)
- add M4 as dep for flex 2.6.x (#3542, #3550)
- add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (#3548)
- make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (#3556)
- add missing patches for extensions in Python 3.x easyconfigs (#3557)
- add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (#3568)
- enable running of tests for HPCG (#3578)
- fix buildopts in tabix easyconfigs (#3584)
v2.8.2 (July 13th 2016)
-----------------------
bugfix release
- added example easyconfig files for 54 new software packages:
Amber (#3200), Bullet (#3175), CONTRAlign (#690), Cluster-Buster (#3191), damageproto (#3222, #3308),
DCA++ (#3219), EIGENSOFT (#3147, #3163), Extrae (#507), fdstools (#3237), ffnet (#3273), GP2C (#3257),
Gurobi (#3239), gc (#3202, #3261), gputools (#546), IMa2p (#3300), IOzone (#3253), i-cisTarget (#3191, #3194),
icmake (#3243), io_lib (#3255), Kent_tools (#3191), libcmaes (#3256), libpsortb (#3259), libxsmm (#3099),
MEGACC (#3263), MM-align (#1428), MOSAIK (#880), MView (#1345), MySQL-python (#3172, #3189), magma (#3219),
mrFAST (#862), mrsFAST (#862), mysqlclient (#3172, #3232), NTL (#3183), PARI-GP (#3257), Paraver (#508),
psutil (#3171, #3231), PSI4 (#3293), Qwt (#3157), RMBlast (#3142), STAMP (#3191), Seqmagick (#3264),
splitRef (#946), TAU (#509), TRF (#3141), TVB (#3053, #3247, #3251), TVB-deps (#3053, #3247, #3251),
tvb-data (#3053, #3247, #3251), tvb-framework (#3053, #3247, #3251), tvb-library (#3053, #3247, #3251),
VampirTrace (#509), Voro++ (#3174), wheel (#3235), wxPropertyGrid (#508), xonsh (#3159)
- added easyconfigs for update of common toolchains: foss/2016b (#3271), intel/2016b (#3270)
- added new easyconfigs for existing toolchains: CrayGNU 2016.03 & 2016.04 (#3291), foss/2016.06 (#3184), intel/2016.03-GCC-5.4 (#3185)
- added additional easyconfigs for various supported software packages, including:
Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2,
Python 2.7.12, Python 3.5.2, Qt 3.3.8, R 3.3.1
- various enhancements, including:
- use check_conflicts function in easyconfigs tests (#2981)
- also include vsc-install in list of sources for recent EasyBuild easyconfigs, to support offline installation (#3203)
- enable building of libmysqld.* in MariaDB easyconfigs (#3230)
- add ALDEx2, phyloseq to bundles for Bioconductor 3.2 (#3211, #3241)
- add biom, geepack, lubridate, pim to list of R 3.2.3 extensions (#3186, #3211, #3275)
- various bug fixes, including:
- add patch for Boost 1.60.0 to fix bug resulting in TypeError (#3162)
- add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU (#3176)
- fix location of libelf.h, only (also) installed as include/libelf.h is there's no /usr/include/libelf.h (#3201)
- fix software name for Guile & GnuTLS (was 'guile' & 'gnutls') (#3207)
- added missing space in Geant4 configopts to specify -DGEANT4_INSTALL_DATA (#3209)
- fix Cython download URL in Python 2.7.11 easyconfigs (#3212)
- add missing build deps for X stack in easyconfigs using foss/2016a or intel/2016a (#3222, #3308)
- fix overruling of exts_list in Perl 5.22.2 easyconfig (#3224)
- add missing dependency on GMP in R 3.2.3 easyconfigs (#3226)
- don't hard specify toolchain for binutils build dep in likwid easyconfig, since it matches parent toolchain (#3240)
- fix homepage & source_urls in HMMER easyconfigs (#3246)
- stick to pydot 1.1.0 for Python 2.6 in Travis config (#3282)
- add python-dev(el) to osdeps in GC3Pie easyconfigs (#3310)
v2.8.1 (May 30th 2016)
----------------------
- added example easyconfig files for 13 new software packages:
drFAST (#906), git-lfs (#2478), grabix (#3127), JWM (#3007), libcroco (#3007), librsvg (#3007), MaCH (#3136),
mayavi (#3106), OpenMM (#2762), Pysam (#3080), SeqPrep (#3097), vt (#3128), wkhtmltopdf (#3098)
- added new easyconfigs for existing toolchains: intel/2016.03-GCC-4.9 (#3088)
- added additional easyconfigs for various supported software packages, including:
Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 update 3
- various bug fixes, including:
- apply libreadline patch to fix bug triggering segmentation fault (#3086)
v2.8.0 (May 18th 2016)
----------------------
feature + bugfix release
- added example easyconfig files for 69 new software packages:
ALPS (#2888), annovar (#3010), BayeScEnv (#2765), BayesAss (#2870), BerkeleyGW (#2925), Blitz++ (#2784, #3004),
bam-readcount (#2850), Commet (#2938), CrossTalkZ (#2939), cuDNN (#2882), DBus (#2855), DFT-D3 (#2107),
DIAL (#3056), dask (#2885), dbus-glib (#2855), FFLAS-FFPACK (#2793), FLAC (#2824), FLANN (#3015, #3029),
FLEUR (#3043), GConf (#2855), GROMOS++ (#1297), GST-plugins-base (#2855), GStreamer (#2855), GTOOL (#2805),
Givaro (#2793), gdist (#2935), gromosXX (#1297), HISAT2 (#2809), i-PI (#2940), Kraken (#3037, #3041), LAME (#2823),
LASTZ (#3002), LinBox (#2793), Loki (#2839), libQGLViewer (#2923, #3008), libXxf86vm (#2855),
MDSplus (#2787, #2838, #3027), MRIcron (#2831), Mawk (#2732), minieigen (#2839), mpmath (#3058), NBO (#3047, 3048),
NGS (#2803), NGS-Python (#2810), ncbi-vdb (#2808), OptiX (#2795), PCL (#3024), PEAR (#2731), PLplot (#2990),
Postgres-XL (#2891), PyGTS (#2969), RSeQC (#2788), Rust (#2920, #2943), rainbow (#2730), SHAPEIT (#2806),
SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665),
travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855),
Yade (#2839), Yambo (#2932)
- add test configuration for Travis (#2942, #2944, #2954, #3061)
- added easyconfigs for new PGI-based toolchains
- pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044), CrayPGI/2016.04 (#2927)
- added new easyconfigs for existing toolchains:
foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181,
LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8
- various other enhancements, including:
- enhance ORCA easyconfig for compatibility with SLURM (#1819)
- enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764)
- clean up binutils easyconfigs to use binutils easyblock (#3006)
- add include/GraphicsMagick to $CPATH in GraphicsMagick easyconfigs (#3034)
- update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050)
- various bug fixes, including:
- fix Perl extensions download urls (#2738)
- add Autoconf as build dep for GCCcore (#2772)
- fix versions of extensions in Bioconductor 3.2 bundles (#2769)
- fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874)
- use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812)
- add zlib as explicit dep in Tk easyconfigs (#2815)
- consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816)
- fix homepage and description in Pygments easyconfigs (#2822)
- include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827)
- consistently use XORG_*_SOURCE constants (#2829, #2830, #2848)
- update source URLs in ScientificPython easyconfig files (#2847)
- add checksums in SuiteSparse easyconfigs (#2849)
- fix build deps for GObject-Introspection (#2852)
- correctly specify Perl location in git easyconfig (#2866)
- fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880)
- fix Perl dependency in worker easyconfig, it requires non-standard Perl modules (#2884)
- add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887)
- fix download URL for packmol (#2902)
- drop usempi toolchain in numexpr easyconfigs, not needed (#2937)
- fix use of resolve_dependencies in tests according to changes in framework (#2952)
- add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (#2967)
- add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (#2971)
- add xproto build dependency for makedepend v1.0.5 (#2982)
- disable parallel build for Doxygen (#2986)
- fix source URLs for FreezeThaw and Tie::Function extensions for Perl v5.22.1 (#2988)
- add sed command in worker easyconfig files to fix module_path in conf/worker.conf (#2997, #3000)
- drop toolchainopts from Eigen easyconfigs, since it is headers-only (#3025)
- clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ (#3036)
- use %(pyshortver)s template rather than hardcoding 2.7 in VTK easyconfigs (#3052)
- correct install location of OpenCV Python bindings (#3054)
- include XZ as dependency for libunwind (#3055)
- add patch to fix broken OpenSSL tests due to expired certificates (#3057)
- fix broken link to VSC website in license headers (#3062)
v2.7.0 (March 20th 2016)
------------------------
feature + bugfix release
- added example easyconfig files for 63 new software packages:
ATSAS (#616, #2587), astropy (#2724, #2727), attr (#2706), BamUtil (#2654), BBMap (#2322), BH (#2508),
CheMPS2 (#2445), CosmoloPy (#2723, #2727), csvkit (#2639), Firefox (#2648), FreeXL (#2422), GL2PS (#2667),
Glade (#2631), htop (#2538), IGV (#2019), IGVTools (#2019), ImageMagick (#2438), jModelTest (#2529),
KEALib (#2420), libcerf (#2656), libgcrypt (#2201), libglade (#2631), libgpg-error (#2201), libspatialite (#2431),
LittleCMS (#2438), MAST (#2542), MLC (#2577), MPJ-Express (#2529), mutil (#2201), neon (#758), NextClip (#2544),
npstat (#2686, #2703), Octopus (#2643), QuickFF (#2721), p4vasp (#2328), PCMSolver (#2445), PFFT (#2643),
PHYLIP (#2694), pkgconfig (#2475, #2476), Platypus (#2618), pplacer (#1056), PRINSEQ (#2437, #2444, #2585),
PyFFmpeg (#2501, #2519), PyGObject (#2443), PyGTK (#2443), PyOpenGL (#2628), pyringe (#2533), qrupdate (#2675),
rgeos (#2635), rpmrebuild (#2402), shift (#2201), SNAPE-pooled (#2688), SNPhylo (#2701), sratoolkit (#2715),
STAR-Fusion (#2463), statsmodels (#2719), StringTie (#2527), synchronicity (#2508), testpath (#2461),
USEARCH (#2537), VarScan (#2464), vsc-install (#2165), Whoosh (#2725), xprop (#2645)
- added new easyconfigs for existing toolchains:
intel/2016.02-GCC-4.9 (#2620), gmpolf/2016a & gmvolf/2016a (#2589)
- stable Cray-specific easyconfigs
- delete deprecated Cray toolchains and easyconfig files (#2400)
- don't hardcode PrgEnv version, remove craype and fftw components in Cray toolchains (#2554)
- remove -XC versionsuffix for stable definitions for Cray* toolchains (#2714)
- support for various software packages with CrayGNU and CrayIntel toolchains: CP2K, GROMACS, WRF
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1,
R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1
- various other enhancements, including:
- copy contrib dir in Velvet easyconfigs so scripts are also available (#2456)
- redefine matplotlib 1.5.1 easyconfig as a bundle, also include cycler extension (dep for matplotlib) (#2470)
- add bitstring extension to Python 2.7.11 easyconfigs (#2471)
- enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (#2473)
- add custom sanity check for libjpeg-turbo (#2480)
- add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (#2495, #2729, #2733)
- add source URL in RAxML 7.2.6 easyconfigs (#2536)
- update MPICH easyconfigs to use new MPICH easyblock (#2589)
- free libX11 & co from unneeded Python dependency/versionsuffix (#2549, #2563, #2605, #2664)
- add '--enable-utf --enable-unicode-properties' configure options in PCRE easyconfigs (#2561)
- required for latest R versions
- add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (#2553, #2578)
- add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (#2547, #2556)
- update psmpi easyconfig files to use the new psmpi easyblock (#2619)
- add easyconfig for Python 2.7.11 on top of X11-enabled Tk (#2614, #2621)
- add virtualenv as extension in Python 2.7.11 easyconfigs (#2660)
- various bug fixes, including:
- fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (#2468)
- don't hardcode CC/CXX in OpenMPI easyconfigs (#2472)
- remove Google Code source URL for mpi4py (#2474)
- rename ffmpeg to FFmpeg (#2425, #2481)
- use available easyblock for flex (#2486)
- fix determining list of easyconfigs in unit test suite, don't assume locations are correct (#2530)
- fix specifying DB dependency in DB_File easyconfigs (#2539)
- remove hard-coded -xSSE4.2 for numpy/scipy with Intel compilers (#2546)
- fix license headers: Hercules foundation is now FWO (#2550)
- add --with-zlib configure argument in libxml easyconfigs (#2555)
- don't hardcode optarch=True in xextproto/xtrans easyconfigs (#2601)
- change toolchain version to '' in easyconfigs that use dummy toolchain and include dependencies (#2612)
- GLib doesn't require libxml2 with Python bindings (#2632)
- add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '--' in build path (#2634)
- add missing 'pkgconfig' dependency for h5py (#2476, #2650)
- correct software name in FastQC easyconfigs (was 'fastqc'), use 'dummy' toolchain for all FastQC version (#2657, #2666)
- add missing libxml2 dependencies in GLib easyconfigs (#2658)
- fix Xerces-C++ download location (#2668)
- enable XML::Bare extension in all Perl easyconfigs (#2672)
- update dead link for SuiteSparse (#2679)
- remove custom exts_filter in easyconfigs used PythonPackage easyblock (#2683, #2685)
- add M4 as build dep for binutils & flex (#2681)
- add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (#2704)
- fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (#2707)
- style cleanup in various easyconfigs (#2378, #2387, #2395, #2396, #2488-#2493, #2496-#2500, #2502-#2504, #2602)
- working towards automated style review of pull requests
v2.6.0 (January 26th 2016)
--------------------------
feature + bugfix release
- add easyconfigs for foss/2016a and intel/2016 common toolchains (#2310, #2311, #2339, #2363)
incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains
- added example easyconfig files for 21 new software packages:
BLASR (#922), BioKanga (#2247), BoltzTraP (#2365), basemap (#2221), CppUnit (#2271), EggLib (#2335),
FLASH (#2281), GLM (#2288), hub (#2249), MACS2 (#1983), MotEvo (#843), numba (#2243), PGI (#1833, #2367),
PLY (#2305), PaStiX (#2319, #2326), patchelf (#2327), pip (#2284), RSEM (#2316), RcppArmadillo (#2289),
SCDE (#2289), slepc4py (#2318)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0,
LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2,
Trinity 2.1.1, VTK 6.3.0
- various other enhancements, including:
- added new Cray* toolchain versions with pinned dependency versions (#2222)
- don't hardcode .so, use SHLIB_EXT constant instead (#2245)
- add custom sanity check in GEOS easyconfigs (#2285)
- various bug fixes, including:
- add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (#2096)
- remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (#2323)
- various style fixes, including:
- get rid of tabs (#2302)
- remove trailing whitespace (#2341)
v2.5.0 (December 17th 2015)
---------------------------
feature + bugfix release
- add GCCcore easyconfig that can be used as base for all compilers (without getting in the way) (#2214)
- + easyconfig for GCC/4.9.3-2.25: bundle of GCCcore 4.9.3 and binutils 2.25
- intended to replace the GNU toolchain
- added example easyconfig files for 39 new software packages:
DIRAC (#2212), GeoIP (#2172, #2185), GeoIP-C (#2172, #2185), graph-tool (#1591), gtkglext (#2217),
Intel Advisor (#2210), InterProScan (#2225, #2227, #2234), intltool (#2136), kallisto (#2173), LibUUID (#1930),
LuaJIT (#2153), libXcursor (#2136), libXrandr (#2136), libXtst (#2143), libdap (#1930), libtasn1 (#2208),
libxkbcommon (#2136), MRtrix (#2217, #2218), MultiNest (#2166, #2168), Nipype (#2150), PPfold (#2183, #2187),
p11-kit (#2208), pangox-compat (#2217), Qt5 (#2136), randrproto (#2136), rhdf5 (#2175), Stampy (#2180, #2182),
scikit-umfpack (#2061), scp (Python pkg) (#2196), sleuth (#2175), traits (#2150), vincent (#2169, #2185),
XKeyboardConfig (#2136), xcb-util (#2136), xcb-util-image (#2136), xcb-util-keysyms (#2136),
xcb-util-renderutil (#2136), xcb-util-wm (#2136), zlibbioc (#2175)
- added new easyconfigs for existing toolchains:
intel/2015.08 (#2194), intel/2016.00 (#2209), intel/2016.01 (#2219), iomkl/2015.03 (#2155)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0,
OpenFOAM 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11
- various other enhancements, including:
- add tidyr to R 3.2.1 easyconfigs (#2174)
- enable C++ support in MIGRATE-N (#2178)
- also installed shared libraries for AMD and UMFPACK in SuiteSparse (#2061)
- fix software name for ParaView (was: Paraview) (#2132)
- enable building of shared libraries for binutils (#2133)
- harden binutils built with dummy toolchain by linking to system libraries via RPATH (#2228)
- enhance easyconfig unit tests to check that each easyconfig file is in the right subdirectory (#2232)
- various bug fixes, including:
- fix ALADIN patch file to not use relative paths, and adjust list of ALADIN sources accordingly (#2207, #2213)
- rename patch files for OpenFOAM to be in line with other patches (#2226)
- fix typo in bzip2 source URLs (#2204)
- force linking of ncurses in libreadline (#2206)
- enable -fPIC in all zlib 1.2.8 easyconfigs (#2220)
- move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right location (#2232)
- restrict parallel build in OpenFOAM-Extend easyconfigs via 'maxparallel', not 'parallel' (#2233)
v2.4.0 (November 10th 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 45 new software packages:
animation (#2007), ANSYS CFD (#1969), ANTLR (#1191, #1980), APR (#1970), APR-util (#1970), Aspera Connect (#2005),
ChIP-Seq (#2119), deap (#2082), DISCOVARdenovo (#1932), FastQC (#1984), fontsproto (#1618, #2038),
GraphicsMagick (#2007), HBase (#1990), ISIS (#1972), libedit (#293), libfontenc (#1618, #2038), libGLU (#1627),
libXdamage (#1618, #2038), libXfont (#1618, #2038), LLVM (#1620, #1989, #2031), MIGRATE-N (#1944), MIRA (#1938),
mympingpong (#2049), MySQLdb (#2011), NCO (#1191, #1980), NIPY (#2064), Nilearn (#2064), NiBabel (#2064),
PBZIP2 (#1038), PIL (#2062), PhyloCSF (#2018), pycairo (#2085), pydicom (#2063), Salmon (#2051), Samcef (#1941),
scikit-image (#1974, #2006), Serf (#1970), SSAHA2 (#1039), Subversion (#1970), SWASH (#2059, #2128), time (#1954),
Trim_Galore (#1984), Trimmomatic (#1987), WEKA (#1986), x264 (#2017)
- added new easyconfigs for existing toolchains: gimkl/2.11.5 (#2093)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0,
ncurses 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, QuantumESPRESSO v5.2.1
- various other enhancements, including:
- enable 'pic' toolchain option in libxml2 easyconfigs (#1993)
- extend list of R libraries included in R v3.2.1 easyconfigs (#2042, #2046, #2067, #2072)
- add Rsubread in Bioconductor easyconfigs (#1971)
- various bug fixes, including:
- fix software name for BEEF (was 'libbeef') (#1679)
- add patch to install qhull.pc (pkgconfig) file with Qhull (#1975)
- don't enable experimental nouveau API in libdrm easyconfigs (#1994)
- fix dev version to follow PEP-440, as required by recent setuptools versions (#1997)
- required to avoid that setuptools transforms the version itself
- see also https://www.python.org/dev/peps/pep-0440/#developmental-releases
- correct homepage in Cufflinks easyconfigs (#2060)
- fix imports for set_tmpdir in easyblock unit tests after function was moved in EasyBuild framework (#2097)
- add patch for Tk 8.6.4 to fix problem with tk.tcl not being found (#2102)
- don't use %(version)s template in toolchain version, causes problems with HierarchicalMNS (#2104)
- fix sanity check paths in several easyconfig (#2109, #2120, #2121, #2125)
- required because of bug fix in sanity_check_step implementation
- CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, Pyke, pandas, pycosat, pyhull, pymatgen,
python-dateutils, Seaborn, Theano, XML-LibXML, XML-Simple
v2.3.0 (September 2nd 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 19 new software packages:
ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780),
gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677),
Molpro (#1880), NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859)
- added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696)
add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1,
Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0
- various other enhancements, including:
- enhance texinfo easyconfig w.r.t. texmf, only use it as a build dependency (#1840)
- enable building of ld.gold in binutils 2.25 (#1885)
- various bug fixes, including:
- fix enabling MPI support for h5py 2.5.0 (#1825)
- fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917)
- put dummy values in place for builddir/installdir templates in easyconfigs unit tests (#1835)
- fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875)
- add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858)
- specify installation prefix for SIP (#1888, #1892)
- add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909)
- required because of fix in EasyBuild framework, causing default sanity check paths to be considered
for extensions that are installed as a module
- affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql,
evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx,
ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn,
SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck
- don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911)
- add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925)
v2.2.0 (July 15th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 62 new software packages:
ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171),
Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995),
EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440),
frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762),
GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760),
libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116),
ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412),
Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776),
rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658),
SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512),
VampirServer (#512), verifyBamID (#1675)
- added easyconfigs for 4 new software bundles:
R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759),
R-bundle-pbd (#1659)
- added easyconfigs for new GNU toolchain (#1346, #1669)
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added example easyconfig for generating buildenv module (#1503)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1,
Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1
- various other enhancements, including:
- update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337)
- update PDT easyconfigs to use PDT easyblock (#1687)
- add custom sanity_check_paths in libxml2 easyconfigs (#1690)
- enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761)
- include snappy as dependency in Hadoop easyconfigs (#1758, #1773)
- enable SSL support in CMake v3.2.3 easyconfigs (#1784)
- add additional extensions in R easyconfigs (#1637)
- various bug fixes, including:
- add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631)
- fix issue with OpenMPI dependency in ECore easyconfigs (#777)
- don't run the Bloom tests for Jellyfish, they can randomly fail (#1016)
- fix source URLs in BioPerl easyconfigs (#1075)
- patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576)
- consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722)
- include Tcl and Tk as dependencies in R easyconfig (#1623)
- add patch for installing paycheck as Py3 extension (#1629)
- add Perl dependency in git 2.x easyconfigs (#1631)
- fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635)
- fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652)
- include Tk as dependency in Python 2.7.9 easyconfigs (#1654)
- include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655)
- drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657)
- include missing libxml2 dep in GLib easyconfigs (#1666)
- fix source URLs in Qt easyconfigs (#1673)
- fix source URLs for argparse Python extension (#1697)
- fix source URLs for deap Python extension (#1699)
- fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708)
- fix names for Xmipp easyconfigs and patches (#1719)
- add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734)
- add M4 as build dep for GCC 5.1.0 (#1735)
- fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748)
- remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765)
- fix source_urls in netCDF easyconfigs (#1766)
- fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767)
v2.1.1 (May 18th 2015)
----------------------
bugfix release
- added example easyconfig files for 3 new software packages:
networkx (#1592), Platanus (#1597), SaguaroGW (#1600)
- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40
- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3
- various bug fixes, including:
- enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590)
- use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595)
- only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609)
v2.1.0 (April 30th 2015)
------------------------
feature + bugfix release
- added example easyconfig files for 27 new software packages:
AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530),
mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036),
Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536),
seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369),
Xmipp (#1489)
- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE
- initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558)
- see also http://easybuild.readthedocs.io/en/latest/Cray-support.html
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1
- various other enhancements, including:
- include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540)
- include SQLite as dependency in Python v2.7.9 easyconfigs (#1468)
- set $LD_PRELOAD for Hoard and jemalloc (#1470)
- fix homepage in SCOTCH easyconfigs (#1485)
- adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510)
- enable pic toolchain option in expat easyconfigs (#1562)
- extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568)
- various bug fixes, including:
- adding missing zlib dependency in all Tcl easyconfig files (#1344)
- fix homepage in FLUENT easyconfigs (#1472)
- use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511)
- stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512)
- replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532)
- stop relying on $MKLROOT in ROOT easyconfigs (#1537)
- use proper Bundle easyblock for biodeps/PRACE (#1566)
- make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574)
- add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574)
v2.0.0 (March 6th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 29 new software packages:
bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568),
fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389),
jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242),
rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370),
ZPAQ (#1242)
- added easyconfigs for new (common) toolchains
foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238),
intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401)
- added new software bundle: Autotools (#1385)
- various other enhancements, including:
- don't define $LDSHARED in zlib easyconfigs (#1350)
- this fixes the long-standing "no version information available" issue with zlib
- see also https://github.com/easybuilders/easybuild-framework/issues/108
- add unit test to check that all extra_options keys are defined in EasyConfig instance (#1378)
- add source MD5 checksums in all GCC easyconfigs (#1391)
- speeding up the unit tests by avoiding rereading of same easyconfig file (#1432)
- fix conflict detection in unit tests by considering build deps separately from runtime deps (#1447)
- fix toolchain for Bison build dep in MVAPICH2-1.9-iccifort-2011.13.367.eb easyconfig (#1448)
- use Bundle generic easyblock for HPCBIOS bundles and fix moduleclass (#1451)
- various bug fixes, including:
- revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144)
- added Java dependencies to EMBOSS easyconfigs (#1167)
- don't list 'lto' as a language in GCC easyconfigs (#1286)
- related to the fixes in the GCC easyblock, see easybuilders/easybuild-easyblocks#535
- rename libint2 easyconfigs as Libint v2 easyconfigs (#1287)
- fix mpi4py source_urls in Python easyconfigs (#1306)
- consistently use CLooG 0.18.0 for GCC 4.8 series (#1392)
- rename GenomeAnalysisTk easyconfigs to GATK (#1399)
- include openssl-devel SLES11 OS dependency in cURL/MySQL/Python easyconfigs (#1422)
- add missing Perl dependency in parallel easyconfigs (#1430)
- correct name in BLAST+ easyconfigs (#1443)
- fix name for sparsehash easyconfigs (#1452)
v1.16.2.0 (March 6th 2015)
--------------------------
(no changes compared to v1.16.1.0, simple version bump to stay in sync with easybuild-easyblocks)
v1.16.1.0 (December 19th 2014)
------------------------------
- set default easyblock to ConfigureMake in TEMPLATE.eb (#1277)
v1.16.0.0 (December 18th 2014)
------------------------------
feature + bugfix release
- added example easyconfig files for 39 new software packages:
ANTs (#1232), BEOPS (#1264), Chhimera (#1255), ctffind (#1249), DBD-SQLite (#1064), DBD-mysql (#1063),
DIALIGN-TX (#668), ffmpeg (#1088), GObject-Introspection (#1079), GTS (#1079), Graphviz (#1079), GraphViz2 (#1079),
grace (#1131), HarfBuzz (#1079), HTSlib (#1161), GSSAPI (#1048), Kerberos_V5 (#1048), libevent (#1063),
libXdmcp (#1129), libXft (#1017), libXinerama (#1017), libXrender (#1017), Maven (#1094), MySQL (#1063),
Net-LibIDN (#1060), OpenCV (#1088), OpenMD (#1105), Qhull (#1105), Pango (#1079), psmpi (#1245, #1246),
RELION (#1017), renderproto (#1017), rjags (#1125), runjags (#1125), SPRNG (#1138, #1141), xineramaproto (#1017),
XML-Dumper (#1061), XML-Parser (#1061), XML-Twig (#1061)
- added easyconfigs for new toolchains
intel/2014.10 & intel/2014.11 (#1219), intel-para/2014.12 (#1246), gpsolf/2014.12 (#1245), iompi/6.6.4 (#1215)
- include easyblock = 'ConfigureMake' in relevant easyconfigs to deal with deprecation of automagic fallback to ConfigureMake (#1248)
- see also easybuild-framework#1113 and Automagic fallback to ConfigureMake
- clean up use of deprecated functionality in existing easyconfigs (#1252, #1259)
- stop using deprecated makeopts, premakeopts and shared_lib_ext
- check for use of deprecated functionality in easyconfigs unit tests
- see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters
- various other enhancements, including:
- also build fftw3_threads libraries, and enhance sanity checks (#1013)
- add unit test to verify specified sanity_check_paths (#1119)
- update and clean up README, refer to http://easybuild.readthedocs.org documentation (#1184, #1224)
- various bug fixes, including:
- fix unit tests w.r.t. changes in framework (#1146)
- remove unnecessary build dependencies for OpenMPI (#1168)
- remove duplicate line in OpenMPI easyconfigs (#1207)
- fix affiliation/mail address for Fotis in headers (#1237)
- fix permissions of easyconfig files for consistency (#1210)
- disable symbol lookup feature in cairo to fix build on SL6 (#1241)
- fix easyconfig gmpolf toolchain w.r.t. MPICH software name (#1217)
- see also easybuild-framework#1112
- fix source_urls for WRF and WPS (#1225)
- fix and clean up GATE easyconfigs (#1228)
- fix broken CLHEP builds by including -gcc in $CXXFLAGS (#1254)
- add patch to fix broken test in Go (#1257)
- fix name of GMAP easyconfigs, should be GMAP-GSNAP (#1268)
- fix easyconfig filenames, enhance unit test to check easyconfig filenames (#1271)
v1.15.2.0 (October 7th 2014)
----------------------------
bugfix release
- disable parallel build for slalib (#968)
- fix compatibility of goolfc with HierarchicalMNS by using GCC toolchain for installing CUDA (#1106, #1115)
- fix zlib OS dependency spec for Debian in Boost easyconfigs (#1109)
- fix compatibility of gimkl with HierarchicalMNS by using gimpi subtoolchain (#1110)
- make both GCC and Clang first-class members in Clang-based toolchains to fix compatibility with HierarchicalMNS (#1113)
v1.15.1.0 (September 23rd 2014)
-------------------------------
bugfix release
- minor bug fixes, including:
- use SHLIB_EXT in GMP/MPFR easyconfigs (#1090)
- fix TopHat homepage and source_urls since page moved (#1092)
- make iomkl toolchain compatible with HierarchicalMNS (#1099)
v1.15.0.0 (September 12th 2014)
-------------------------------
feature + bugfix release
- added example easyconfig files for 13 new software packages:
Circos (#780), DB_File (#913), Emacs (#970), evmix (#1077), GD (#780), gsl (#1077), IOR (#949), JAGS (#1076),
libgd (#780), MethPipe (#1070), Modeller (#825), NAMD (#835), netCDF-C++4 (#1015)
- added easyconfigs for new toolchains (#986, #1051):
gimkl/1.5.9, ictce/7.1.2
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ...
- various enhancements, including:
- make existing ictce/intel toolchains compatible with HierarchicalMNS (#1069)
- this involves installing impi with an iccifort toolchain, and imkl with an iimpi toolchain
- various bug fixes, including:
- download link for Perl modules changed to use cpan.metapan.org
- fix missing MPI-based OpenFOAM libraries (Pstream, (pt)scotchDecomp), make sure provided SCOTCH is used (#957)
v1.14.0.0 (July 9th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 17 new software packages:
ANSYS (#836), Beast (#912), ELPH (#910, #911), FastTree (#900, #947), GEM-library (#858), HPCG (#853),
mdtest (#925), ncview (#648), PRANK (#917), RDP-Classifier (#903), SDPA (#955), SIBELia (#886),
SOAPaligner (#857), SPAdes (#884), stemming (#891), WHAM (#872), YAXT (#656)
- added easyconfigs for new toolchains (#935, #944, #948):
foss/2014b, ictce/6.3.5, intel/2014b
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- various enhancements, including:
- replace use of deprecated (pre)makeopts with (pre)buildopts in all easyblocks (#954)
- disable running embossupdate on installation of EMBOSS (#963)
- various bug fixes, including:
- really enable OpenMP support in FastTree easyconfigs (#947)
- fix easyconfigs unit tests after changes in framework (#958)
v1.13.0.0 (May 29th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 32 new software packages:
APBS (#742), BayesTraits (#770), bc (#888), BitSeq (#791), CEM (#789), CVS (#888), eXpress (#786), file (#888),
GEMSTAT (#861), GMAP (#594), Go (#887), iscp (#602), IsoInfer (#773), Jellyfish (#868), less (#888),
libcircle (#883), mcpp (#602), MMSEQ (#795), MUSTANG (#800), OpenFOAM-Extend (#437), popt (#759), pscom (#759),
psmpi2 (#759), QuadProg++ (#773), rSeq (#771), RSEQtools (#870), Ruby (#873), segemehl (#792), SOAPec (#879),
SOAPdenovo2 (#874), SRA-Toolkit (#793), texinfo (#888)
- added easyconfig for new toolchain goolfc/1.4.10
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- e.g. older versions of Boost (1.47.0), GCC (4.1-4.4), & recent versions of Clang, GCC, Lmod, etc.
- various enhancements, including:
- add OpenSSL dependency for cURL, to enable HTTPS support (#881)
- also install esl-X binaries for HMMER (#889)
- various bug fixes, including:
- properly pass down compiler flags for ParMGridGen (#437)
- specify proper make options for PLINK, fixing the build on SL6 (#594, #772)
- fix netloc version (0.5 rather than 0.5beta) (#707)
- remove Windows-style line ending in netCDF patch file (#796)
- bump version of OpenSSL dep for BOINC (#882)