forked from easybuilders/easybuild-easyconfigs
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathRELEASE_NOTES
3246 lines (3010 loc) · 226 KB
/
RELEASE_NOTES
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
For more detailed information, please see the git log.
These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html.
The latest version of easybuild-easyconfig provides 12,266 easyconfig files, for 2,349 different software packages,
incl. 36 different (compiler) toolchains.
v4.4.0 (June 2nd 2021)
----------------------
feature release
- added easyconfigs for new Fujitsu toolchain: FCC/4.5.0 (#12999, #12995, #13007), ffmpi/4.5.0 (#13000) and Fujitsu/21.05 (#13001, #13007)
- add easyconfigs for updates of common toolchains: foss/2021a (#12867, #12975), intel/2021a (#12885, #12975)
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added easyconfig for gomkl/2021a toolchain (#12987)
- added example easyconfig files for 58 new software packages:
- Archive-Zip (#12651), BirdNET (#12737, #12712, #12737), cell2location (#12448), cryoDRGN (#12704),
dm-reverb (#12824), DROP (#12559, #12801, #12950), fastahack (#12841), fermi-lite (#12856), filevercmp (#12841),
FlexiBLAS (#12476), freetype-py (#12918), fsom (#12841), garnett (#12529), gawk (#12716), gemmi (#12855),
georges (#12570), hifiasm (#12897), intervaltree (#12838), LDC (#12671), libidn2 (#12670), librosa (#10477),
librsb (#12780), line_profiler (#12556), loompy (#12804), mmtf-cpp (#12580), mongolite (#12632), msgpack-c (#12580),
multichoose (#12839), networkTools (#12810), NewHybrids (#12528), Octopus-vcf (#12598), onedrive (#12671),
p4-phylogenetics (#12549), pagmo (#12678), pyfaidx (#12872), pyfasta (#12952), pygmo (#12678), pysheds (#12791),
R-INLA (#12955, #12927, #12955), RegTools (#12874), request (#12448), rMATS-turbo (#12982), scanpy (#12731),
SeqLib (#12856), SeuratData (#12993), SeuratWrappers (#12994), smithwaterman (#12841), snp-sites (#12900),
SSW (#12856), tabixpp (#12837), TagDust (#11599), TALON (#12963), tMAE (#12559), TranscriptClean (#12952),
umap-learn (#12448), vcflib (#12841), xESMF (#12799), XlsxWriter (#12820)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.4.1, apex 20210420, astropy 4.2.1, binutils 2.36.1, BLIS 0.8.1, Bonito 0.3.8, BUSCO 5.1.2, canu 2.1.1,
carputils 20210513, CastXML 0.4.3, ccache 4.2.1, CDO 1.9.10, CIRCexplorer2 2.3.8, CLHEP 2.4.4.0, CMake 3.20.1,
CNVkit 0.9.8, CUDA(core) 11.3.0, CuPy 8.5.0, cURL 7.76.0, DFA 2.1.2, Doxygen 1.9.1, Eigen 3.3.9, FastANI 1.33,
FFTW 3.3.9, GATK 4.2.0.0, GCC 10.3.0 + 11.1.0, GDB 10.2, gdc-client 1.6.0, GDRCopy 2.2, Geant4 10.7.1,
Geant4-data 20210510, GeneMark-ET 4.65, glew 2.2.0, GLib 2.68.2, GLPK 5.0, GMP 6.2.1, Go 1.16.3, Graphviz 2.47.0,
GROMACS 2021.2, GStreamer 1.18.4, GTDB-Tk 1.5.0, Gurobi 9.1.2, HMMER 3.3.2, Horovod 0.21.3, hwloc 2.4.1,
hypothesis 6.13.1, IGV 2.9.4, impi 2021.2.0, imkl 2021.2.0, intel-compilers 2021.2.0, JasPer 2.0.28, Julia 1.6.1,
Kraken2 2.1.1, KronaTools 2.8, libarchive 3.5.1, libdeflate 1.7, libdrm 2.4.106, libfabric 1.12.1, libreadline 8.1,
libRmath 4.0.0, libsndfile 1.0.31, LIBSVM 3.24, LibTIFF 4.2.0, libunwind 1.5.0, libwebp 1.2.0, LLVM 11.1.0,
LMDB 0.9.28, LUMPY 0.3.1, lz4 1.9.3, Mako 1.1.4, MATLAB 2021a, Mesa 21.1.1, meshalyzer 2.2, Meson 0.58.0,
MetaBAT 2.15, metaWRAP 1.3, minimap2 2.18, Molden 6.8, MotionCor2 1.4.2, ncview 2.1.8, NetPIPE 5.1.4, nettle 3.7.2,
NiBabel 3.2.1, Nilearn 0.7.1, Nim 1.4.6, Ninja 1.10.2, NLopt 2.7.0, NSS 3.65, numactl 2.0.14, NWChem 7.0.2,
OpenBLAS 0.3.15, openCARP 6.0, OpenEXR 3.0.1, OpenMM 7.5.0, OpenMPI 4.1.1, OpenSSL 1.1 (wrapper),
OSU-Micro-Benchmarks 5.7.1, Pandoc 2.13, parallel 20210322, parasail 2.4.3, PAUP 4.0a168, PCRE2 10.36, Perl 5.32.1,
pigz 2.6, PMIx 3.2.3, Primer3 2.5.0, PRSice 2.3.3, py-aiger 6.1.14, pybind11 2.6.2, PyCharm 2021.1.1, pydot 1.4.2,
pyproj 3.0.1, PySAT 0.1.7.dev1, PyTorch 1.8.1, python-parasail 1.2.4, Pylint 2.7.4, Python 3.9.5, Qt5 5.15.2,
R-keras 2.4.0, rasterio 1.2.3, RAxML-NG 1.0.2, rclone 1.54.1, re2c 2.1.1, ReFrame 3.5.2, Rmath 4.0.4, Rust 1.52.1,
Sambamba 0.8.0, samblaster 0.1.26, samclip 0.4.0, scikit-allel 1.3.2, SciPy-bundle 2021.05, SCons 4.1.0.post1,
snakemake 6.1.0, SQLite 3.35.4, SRPRISM 3.1.2, Tcl 8.6.11, TCLAP 1.2.4, tmux 3.2, tqdm 4.60.0, UCX 1.10.0,
Valgrind 3.17.0, WannierTools 2.5.1, wget 1.21.1, wxWidgets 3.1.4, X11 20210518, x264 20210414, x265 3.5,
xorg-macros 1.19.3, YAXT 0.9.0, zarr 2.8.1, zstd 1.4.9
- minor enhancements, including:
- add additional extensions to R v4.0.3 and v4.0.4: miceadds, visdat, UpSetR, naniar, stringdist,
image.binarization (#12735), lassosum (#12821), lslx, regsem, semPLS (#13005)
- add GenABEL to R-bundle-Bioconductor (#12822)
- various bug fixes, including:
- disable automatic acceptance of NVHPC EULA (#12014)
- enhance RStudio-Server, add patch to inherit environment variables, add sanity check commands to verify installation (#12544)
- add fix to scipy to handle NaN arguments to "vi" function (#12551)
- copy all binaries + examples & co for PAML v4.9j (#12567)
- add patch to fix hardcoded num_cores in DMCfun extension included with R 4.0.x (#12583)
- backport Charm++ patch for NAMD/2.14 on intel/2020a to handle newer glibc (#12594)
- add setuptools_scm and pytest-runner extensions to Pylint easyconfigs (#12599)
- fix typo in Delly easyconfig to actually do parallel build (#12633)
- fix potential memory leak in OpenBLAS 0.3.12 (#12649)
- consistently use pip to install Python packages in recent Python easyconfigs (#12650)
- replace bintray source url for Groovy (#12652)
- add missing Python & Perl dependencies to for AUGUSTUS v3.4.0 with foss/2020b (#12662)
- fix wget dependency: use libidn2 rather than libidn (#12670)
- fix source URLs for recent ELPA versions (#12700)
- override host compiler check in CUDAcore (#12701)
- add Python build dependency to libpsl 0.21.0 easyconfigs (#12715)
- fix error in libgpg-error 1.36 with gawk builtin (#12716)
- add libtool build dependency to leidenalg (#12741)
- fix source URLs for Boost 1.71.0 - 1.74.0 easyconfigs (#12743) and Boost.Python (#12744)
- add patches for PyTorch 1.7.1 avoiding failures on POWER and A100 (#12753)
- add patch for OpenPGM 5.2.122 eaysconfigs to fix non-existent directory in *.pc (pkgconfig) file (#12774)
- add missing Perl build dependency to recent wget easyconfigs (#12787)
- make sure Python dependency is used in preCICE 2.x easyconfigs (#12793)
- don't skip source step in FastTree easyconfigs + fix SHA256 checksum for FastTree 2.1.11 (#12794)
- add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64 (#12836)
- add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 (#12865)
- fix checksum for MaxBin 2.2.7 (#12869)
- run 'make clean' before building FragGeneScan, to clean up object files included in source tarball (#12870)
- clean up install of KronaTools (#12871)
- add UCX dependency to OneAPI versions of impi (#12873)
- correct description in libdeflate easyconfig (#12886)
- override Makefile with hardcoded CC=cc in UnZip easyconfigs (#12887)
- fix compatibility of FLAIR v1.5.1-20200630 with rpy2 v3.x (#12899)
- fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking (#12912)
- fix source URLs in BLAST 2.10.x easyconfigs (#12914)
- add missing xproto build dependency to imake easyconfig (#12930)
- add patch to fix GCC 10.2.0 rejecting valid code on PPC (#12948)
- in easyconfig tests, check version of dependencies named Python, not if dependencies with certain versions are named Python (#12962)
- update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes (#12967, #12988)
- fix download URL for DB 18.1.40 (#12974)
- fix test failure in TensorFlow 2.4.1 on recent CUDA drivers (#12979)
- fix error in configopts for netCDF and HDF5 and add missing dependencies of ABINIT 9.x (#12981)
- add patch to fix buffer overflow in OpenMPI 4.1.x (#12983)
- other changes:
- update setup.py to indicate compatibility with Python 3.8 and 3.9 (#12565)
- add -Java versionsuffix for Hadoop easyconfig using GCCcore/10.2.0 toolchain, since it depends on Java 1.8 (#12709)
- remove unneccessary workaround for missing version of OpenDataCube and Spyder for 2020+ toolchains (#12757)
- remove 'unpack_sources = False' from recent easyconfigs that use a *.whl file as source (#12783)
- whitelist Seaborn 0.10.1 for NanoComp 1.13.1 and NanoPlot 1.33.0 (#12790)
- add check to make sure that source step is not being skipped (#12807)
- use EasyConfig.disable_templating method in test suite (#12848)
- disable usNIC by default in libfabric to avoid problems due to linking to both libnl and libnl-3 (#12854)
- use OpenSSL wrapper as dependency in easyconfigs using GCCcore/10.3.0 toolchain (#12922, #12944)
- dump easyconfig before initializing easyblock in order to compare it with original easyconfig (#12925)
- remove postinstallcmds from imkl 2020.x easyconfigs, easyblock now installs examples (#12937)
v4.3.4 (April 9th 2021)
-----------------------
update/bugfix release
- added easyconfig for goblf/2020b toolchain (#12381, #12535)
- added example easyconfig files for 41 new software packages:
- amplimap (#12205), BEEF (#12104), bpp (#12036), Brotli (#11651), CDAT (#12322), cicero (#12252),
CIF2Cell (#12258), CompareM (#9377), DL_POLY_4 (#12324), DMCfun (#12412), ESMPy (#12339), FLAC (#12300),
gdbm (#12322), GPyOpt (#12524), json-c (#12344), libcdms (#12322), libdrs (#12322), libogg (#12285),
libvorbis (#12300), LncLOOM (#12287), LPJmL (#12344), maze (#12354), MetaEuk (#12188), mrcfile (#12497),
Myokit (#12261), NCCL-tests (#12415), pyABC (#12329), PyCifRW (#12258), PyOD (#12507), pyro-api (#12447),
pyro-ppl (#12447), R-opencv (#12226), Ratatosk (#12443), RevBayes (#12419), sansa (#12354), scikit-cuda (#12352),
Seeder (#9057), suave (#12354), voltools (#12497), vorbis-tools (#12300), YACS (#12309)
- added additional easyconfigs for various supported software packages, including:
- AOCC 3.0.0, Arriba 2.1.0, ArviZ 0.11.1, arpack-ng 3.8.0 BCFtools 1.12, BEDTools 2.30.0, BUSCO 5.0.0, BioPerl 1.7.8,
Blosc 1.21.0, Boost.Python 1.74.0, bitarray 1.2.1, bokeh 2.2.3, CP2K 8.1, CUDAcore 11.2.2, CellRanger 6.0.0,
Clang 11.0.1, DIAMOND 2.0.7, Delly 0.8.7, dask 2021.2.0, dm-tree 0.1.5, Elk 7.0.12, Extrae 3.8.0, FLUENT 2021R1,
FabIO 0.11.0, Fiji 20201104, Flye 2.8.3, FreeSurfer 7.1.1, GDAL 3.2.1, GEOS 3.9.1, GLFW 3.3.3,
GMAP-GSNAP 2020-12-17, GROMACS 2021, GetOrganelle 1.7.4, gmsh 4.7.1, HTSeq 0.11.3, HTSlib 1.12, Hypre 2.20.0,
hyperopt 0.2.5, iVar 1.3.1, igraph 0.9.1, Jansson 2.13.1, Kent_tools 411, LAPACK 3.9.1, LAST 1179, LibSoup 2.72.0,
libxc 5.1.3, MAFFT 7.475, MCR R2020a.6 + R2020b.5 + R2021a.0.eb, MDTraj 1.9.5, MUMPS 5.3.5, MaSuRCA 4.0.1,
Mercurial 5.7.1, Monocle3 0.2.3, NGS 2.10.9, NVHPC 21.2, NetLogo 6.2.0, Nextflow 21.03.0, ncbi-vdb 2.10.9,
OSU-Micro-Benchmarks 5.7, OpenCV 4.5.1, OpenEXR 2.5.5, OptiX 7.2.0, PETSc 3.14.4, PLUMED 2.7.0, PROJ 7.2.1,
PyAMG 4.0.0, PyCUDA 2020.1, PyCairo 1.20.0, PyOpenCL 2021.1.2, PyTorch-Geometric 1.6.3, p7zip 17.03, pFUnit 4.2.0,
picard 2.25.1, pocl 1.6, preCICE 2.2.0, protobuf 2.5.0, pymatgen 2022.0.4, python-igraph 0.9.0, Qtconsole 5.0.2,
R 4.0.4, RASPA2 2.0.41, RDFlib 5.0.0, ReFrame 3.5.1, Ruby 2.7.2, rnaQUAST 2.2.0, SAMtools 1.12, SDL2 2.0.14,
SIMPLE 3.0.0, SPAdes 3.15.2, SUNDIALS 5.7.0, Seurat 4.0.1, Spark 3.1.1, scikit-image 0.18.1, silx 0.14.0,
spglib 1.16.1, sympy 1.7.1, tensorboardX 2.1, tensorflow-probability 0.12.1, tmux 3.1c, USEARCH 11.0.667,
VTK 9.0.1, VTune 2020_update3
- minor enhancements, including:
- verify checksum of all patch files in easyconfigs test suite (#12221)
- add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a (#12227)
- add sanity check commands for vorbis-tools (#12304)
- add extensions to R-bundle-Bioconductor 3.12: motifmatchr (#12390), OUTRIDER + FRASER (#12510)
- add DMCfun extension for R v4.0.3 + v4.0.4 (#12409)
- various bug fixes, including:
- add missing GNU time dependency to WRF 4.0.2 built with foss/2018b (#12179)
- add archive source_urls for Hadoop and Spark (#12220)
- add missing Python build dep for SeqAn 2.4.0 (#12222)
- add missing pkg-config build dependency to VCFtools 0.1.16 (#12245), GObject-Introspection-1.64.0 (#12298), libsndfile (#12303)
- set $HTSLIB_DIR in HTSlib for use by EnsEMBLCoreAPI & Bio-DB-HTS (#12253)
- bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0 (#12277, #12288)
- bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error (#12293)
- skip sanity check test in IPython-7.18.1-GCCcore-10.2.0.eb (#12294)
- add missing Perl and Autotools build dependencies in recent WRF easyconfigs (#12301)
- add missing groff build dependency for Perl 5.30.0 and 5.32.0 (#12307)
- add linkcomm + rnetcarto extensions to R v4.0.3 (#12311)
- add dependency on Flask in all ASE v3.21.1 easyconfigs (#12312)
- remove hard-coded -xHost from MMseqs2-11-e1a1c (#12317)
- revised outdated easyconfigs for libcerf + replaced obsolete homepages and source urls (#12323)
- consistently include 'new_archive' source URL in Qt5 easyconfigs + add missing checksums (#12325, #12426)
- fix source URL and add alternate checksum for Hypre 2.14.0 (#12337)
- add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI (#12340)
- add SourceForge fallback source URL for recent freetype easyconfigs (#12341)
- revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 (#12345)
- use -D_USE_METIS_5p1 in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0 (#12403)
- make sure that path to eb is always found by tests (#12436)
- stop tests changing the EasyBuild easyconfigs (#12454)
- use pip to install pkgconfig 1.5.1 (#12455)
- add CI test checking if the Python default source_urls are used and fix CI check where use_pip=False was ignored (#12456, #12471)
- fix source URLs in Arrow 0.x easyconfigs (#12475)
- fix numpy tests for recent SciPy-bundle easyconfig on POWER (#12481)
- don't download hwloc during FIRESTARTER build (#12482)
- avoid 0.0.0 install version for various Python apps (#12519, #12522)
- enable USER_SDPD package and disable building docs in LAMMPS 3Mar2020 (#12527)
- update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages (#12534)
- add Python 3 build dep for HMMER 3.3.x test step (#12536)
- other changes:
- rename opencv_contrib and update to OpenCV v3.4.1 with contrib versionsuffix (#12229)
- fix minor style issues in POV-Ray v3.7.0.8 easyconfigs (#12342)
- enable -fPIC for g2clib (#12349)
- consistently include Keras-Applications and Keras-Preprocessing extensions in Keras 2.3.1 easyconfigs (#12375)
- remove PYPI_SOURCE source URL from easyconfigs using PythonPackage or PythonBundle (#12541, #12452, #12453)
- require sanity_pip_check for all Python package/bundles (#12464)
v4.3.3 (February 23rd 2021)
---------------------------
update/bugfix release
- add easyconfig for new iibff toolchain: iibff/2020b (#12185)
- added easyconfigs for 6 new toolchains:
- gobff/2020b (#12098), goblf/2018b (#6615), gomkl/2020b (#12198), iimkl/2018a (#6092), iomkl/2019b (#11981), iomkl/2020b (#12009)
- added example easyconfig files for 72 new software packages:
- AOCC (#11868), CHERAB (#7141), CaDiCaL (#11966), CellRanger-ARC (#12114), CuPy (#11749), DFA (#11979),
FIGARO (#11924), FIRESTARTER (#12160), FIt-SNE (#8630), GPyTorch (#12010), GSEA (#10395), GetOrganelle (#11948),
Glucose (#11965), GraPhlAn (#10707), ITSx (#10558), Kaleido (#11998), LAPACK (#6615), LSD2 (#11903),
Lingeling (#11964), MPB (#7026), MiniCARD (#11963), MiniSat (#11962), NGSpeciesID (#11918), NanopolishComp (#11823),
Nsight-Compute (#12043), Nsight-Systems (#12042), PHANOTATE (#8667), PIPITS (#10558), PyClone (#11940),
PySAT (#12000), RNAmmer (#7262), Raysect (#7141), SICER2 (#12200), SOCI (#12045), SeisSol (#7194), SignalP (#11862),
Stack (#11310), SuperLU_DIST (#11693), Teneto (#12056), Transformers (#12032), YANK (#11742), Z3 (#12013),
bgen (#7456, #11867), bgen-reader (#7456, #11867), bpytop (#12040), byobu (#11932), chi2comb (#11867),
cuTENSOR (#11914), dd (#11978), decona (#11891), dicom2nifti (#11955), eccodes-python (#12083), fftlib (#11944),
flatbuffers-python (#12148), fpocket (#11980), gh (#11851), intel-compilers (oneAPI) (#11982), libGDSII (#7026),
libpci (#11871), liknorm (#7456, #11867), limix (#7456, #11867), logaddexp (#11867), neptune-client (#11985),
plinkQC (#12068), preCICE (#11886), py-aiger (#11999), py-aiger-bdd (#11999), pytest-xdist (#11883, #11893),
samblaster (#7378), terastructure (#12197), typing-extensions (#11636), webin-cli (#8674),
- added additional easyconfigs for various supported software packages, including:
- ack 3.4.0, AmberTools 20, AMD-LibM 3.6.0-4, AMD-RNG 2.2, AMD-SecureRNG 2.2, annovar 20191024, ASE 3.21.1,
AUGUSTUS 3.4.0, Bazel 3.7.2, bcgTree 1.1.0, BLAST+ 2.11.0, Bonito 0.3.5, Bowtie2 2.4.2, causalml 0.8.0-20200909,
CGAL 5.2, ConnectomeWorkbench 1.4.2, CUDAcore 11.2.1, cuDNN 8.0.5.39, dcm2niix 1.0.20201102, DendroPy 4.5.2,
DIAMOND 0.9.36 + 2.0.6, ecCodes 2.20.0, ELPA 2020.11.001, Emacs 27.1, FusionCatcher 1.30, gensim 3.8.3, GHC 8.6.5,
gnuplot 5.4.1, GPAW 21.1.0, Graphviz 2.44.1, GROMACS 2020.5, Gurobi 9.1.0, HH-suite 3.3.0, HMMER 3.3.2, HTSlib 1.11,
Horovod 0.21.1, imbalanced-learn 0.7.0, impi 2021.1.1, inferCNV 1.3.3, ITK 5.1.2, IQ-TREE 2.1.2, JasPer 2.0.24,
JUBE 2.4.1, libgit2 1.1.0, libzip 1.7.3, likwid 5.1.0, MariaDB 10.5.8, medaka 1.2.0, Meep 1.6.0, mkl-service 2.3.0,
MPICH 3.3.2, muParser 2.3.2, NanoComp 1.13.1, NanoPlot 1.33.0, networkx 2.5, NLTK 3.5, numba 0.52.0, NVHPC 20.11,
nvtop 1.1.0, OpenCoarrays 2.9.2, OpenFOAM v2012, OpenJPEG 2.4.0, OpenMPI 4.1.0, parasail 2.4.2, PLUMED 2.6.2,
PostgreSQL 13.2, pydicom 2.1.2, PyMC3 3.11.0, python-parasail 1.2.2, PyTorch 1.7.1, QIIME2 2020.11,
QuantumESPRESSO 6.7, QuickFF 2.2.7, R 4.0.3, R-bundle-Bioconductor 3.12, ReFrame 3.4.1, RMBlast 2.10.0, RSEM 1.3.3,
Salmon 1.4.0, scikit-build 0.11.1, SciPy-bundle 2020.03 w/ Python 2.7.18, Seaborn 0.11.1, SEPP 4.4.0,
SHAPEIT4 4.2.0, SpaceRanger 1.2.2, Stacks 2.54, STAR 2.7.7.a, statsmodels 0.12.1, SuiteSparse 5.8.1, tbb 2020.3,
TensorFlow 1.15.5 + 2.4.1, Theano 1.1.2, torchvision 0.8.2, V8 3.4.0, Wannier90 3.1.0
- minor enhancements, including:
- enable building of QtWebEngine in Qt5 easyconfig using foss/2017b or intel/2017b (#7302)
- enable NVPTX offload in GCCcore 9.3.0 easyconfig (#11839)
- also build shared library in recent HDF easyconfigs (#11847)
- add support for HDF4 to GDAL v3.0.2 and v3.0.4 (#11855)
- add patch for magma 2.5.4 with fosscuda/2019b to allow any sm_* value to be passed via GPU_TARGET (#11861)
- add missing M4 build dependency to recent SuiteSparse versions (#11869)
- enable tests for most recent Bazel versions (3.x) (#11894)
- enable gipaw in QuantumESPRESSO 6.6 easyconfig (#11905)
- add RCAL + sensemakr extensions to R 4.0.0 (#11921)
- add additional extensions to R v4.0.3 easyconfig (#11922, #12057)
- improve sanity_check_paths for AMD-LibM (#11933)
- symlink include/lib subdirs + enhance sanity_check_paths for AMD-RNG v2.2-4 (#11934)
- improve sanity_check_paths for AMD-SecureRNG (#11935)
- update Clang 10+ dependencies & build extra tools (#12013)
- add Inline extension to recent Perl easyconfigs (5.30+) (#12029)
- add EnsDb.Hsapiens.v86 to Bioconductor 3.11 (#12078)
- add sanity check command for bam-readcount v0.8.0 to check --version output (#12092)
- add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 (#12174)
- add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (#12136, #12137)
- various bug fixes, including:
- added missing space in 'configopts' in ParaView 5.8.0 easyconfigs using 2020a toolchain (#10989)
- use bfd linker for glibc 2.30 (#11331)
- add missing moduleclass in UCLUST easyconfig (#11477)
- don't disable optarch for Clang 11.0.0 (#11814)
- add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x (#11837)
- fix compilation of TensorFlow 2.3.1 with CUDA and glibc 2.26 on POWER (#11859)
- disable building of manpages for GDCM to fix installation problem with docbook (#11866)
- add patch for LLVM 6.0.0 to fix missing exported symbol LLVMInitializeInstCombine (#11873)
- fix name of source file for GDRCopy v2.1 (#11887)
- fix Tombo to work with rpy2 v3 when creating DataFrames (#11892)
- fix GCCcore 8.1.0 w.r.t. removed sys/ustat.h in glibc 2.28 (#11896)
- add git as a dependency to GitPython version 3.x (#11902)
- fix undefined __ieee128 on ppc64le with glibc 2.26 for magma (#11930) and PyTorch (#11936)
- update Hypre git location for PETSc 3.11.0 using downloaded dependencies (#11947)
- fix source URL in expat easyconfigs (and consistently add custom sanity_check_paths) (#11960)
- use libpng provided by EasyBuild in VTK to fix build issue on ppc64le (#11990)
- add missing pkg-config build dependency for GObject-Introspection v1.66.1 (#11949)
- add missing plotly-orca dependency for NanoPlot (#11967, #12015)
- add patch for Boost 1.74.0 to fix missing include file (#12007)
- fix for "error: 'runtime_error' is not a member of 'std'" in qtlocation for Qt5 v5.14.2 (#12012)
- fix homepage for gnuplot 5.2.8, use http:// since homepage is not reachable via https:// (#12047)
- fix OS dependencies for libfabric (#12058)
- fix vector mul and div with broadcasts in -masm=intel mode in GCCcore v9.3.0 (#12065)
- add missing ESMF dependency in NCO easyconfigs (#12071, #12072)
- add patch to fix version for bam-readcount 0.8.0 (#12075)
- add missing Perl build dep for (recent) libcerf versions, required for 'pod2html' command (#12085)
- add missing bzip2 dependency to recent ncbi-vdb easyconfigs (#12120)
- add missing Perl build dependency for BLIS 0.8.0 (#12146)
- use https://sources.easybuild.io as fallback source URL for UDUNITS (#12049, #12156, #12182)
- correct the GCC version check to allow IBM VSX builds of GROMACS 2020.4 and 2020.5 (#12159)
- add missing mkl-service dependency for Theano built with intel/2019b + enhance sanity check (#12172)
- add patches to fix test problems with p4est 2.2 (#12028)
- fix build of Bison using older system GCC (v4.x) (#12203)
- fix lack of optimisation for SHAPEIT4 v4.1.3 (#12206)
- add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6 (#11801, #12208)
- fix source URL for libspatialite (#12213)
- add 'archive' fallback source URL to MAGMA easyconfigs (#12214)
- fix checksum for patch in make 4.2.1 easyconfig using GCC/7.3.0-2.30 (#12223)
- other changes:
- replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a single easyconfig for BioPP v2.4.1 (using Bundle easyblock) (#11609)
- add CESM-deps to whitelist in check for custom sanity_check_paths (#11916)
- include '-4' in version for AMD-SecureRNG v2.2-4 (#11934, #11935)
- switch to using python-parasail and tqdm dependencies in Bonito easyconfigs (#11937)
- rename orca to plotly-orca (#12015)
- remove duplicate extensions in R 3.5.x easyconfigs, and add test to detect such issues (#12059)
- remove Python dependency from ecCodes v2.17.0 since it doesn't provide Python bindings (#12084)
- update Java/1.8 wrapper to Java 1.8.0_281 (#11928, #12088)
- update Bison (build) dependency for flex built with system compiler to v3.5.3 (#12111)
- make symlinking of posix.so in test suite configuration conditional (#12123)
- move make 4.3 easyconfigs to GCCcore toolchain (#12166)
- move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore (#12168)
- rename SNAP to SNAP-HMM and update easyconfig (#12218)
v4.3.2 (December 10th 2020)
---------------------------
update/bugfix release
- add easyconfigs for new gobff toolchain: gobff/2020.11 + gobff/2020.06-amd (#11761)
- add easyconfigs for updates of common toolchains: foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
- see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html
- added example easyconfig files for 41 new software packages:
- alsa-lib (#11658), assimp (#11759), BioServices (#11602), carputils (#11270), cctools (#11799),
code-server (#11778), CRISPResso2 (#11775), elfutils (#11783), EMU (#11641), fgbio (#11519), Flink (#11747),
FreeSASA (#11699), Geant4-data (#11610), geocube (#11714), IPM (#11768, #11772), libmicrohttpd (#11783),
libStatGen (#7982), libzeep (#11687), LLDB (#11822), meshalyzer (#11270), meshtool (#11270),
Metagenome-Atlas (#11620), MLxtend (#11601), MRChem (#11604), MRCPP (#11579), mxml (#11769), mxmlplus (#11771),
nanocompore (#11690), neon (#11797), Open-Data-Cube-Core (#11713), OpenSees (#11613), PEST++ (#11565),
pyFAI (#11849), pymca (#11848), RE2 (#11718), scikit-bio (#11660), SpaceRanger (#11776), SplAdder (#11607),
SWAT+ (#11615), velocyto (#11744), WCT (#11779)
- added additional easyconfigs for various supported software packages, including:
- BBMap 38.87, Boost 1.74.0, CUDA 11.1.1, CellRanger 5.0.0.eb, CheckM 1.1.3, Clang 11.0.0, cuDNN 8.0.4.30,
DMTCP 2.6.0, FDS 6.7.5, FFmpeg 4.3.1, GROMACS 2020.4, Geant4 10.6.2, Ghostscript 9.53.3, GitPython 3.1.9,
GlobalArrays 5.8, HDF5 1.10.7, h5py 3.1.0, hypothesis 5.41.5, JasPer 2.0.16, LittleCMS 2.11, libedit 20191231,
libyaml 0.2.5, MPFR 4.1.0, magma 2.5.4, matplotlib 3.3.3, NCCL 2.8.3, NLopt 2.6.2, Nextflow 20.10.0,
netCDF-Fortran 4.5.3, OpenBLAS 0.3.12, OpenMolcas 20.10, Pillow 8.0.1, PnetCDF 1.12.1, PyYAML 5.3.1,
packmol 20.2.2, protobuf 3.14.0, psycopg2 2.8.6, pybind11 2.6.0, pycocotools 2.0.2, Qt5 5.14.2, RAxML-NG 1.0.1,
RSeQC 4.0.0, rioxarray 0.1.1, SCOTCH 6.1.0, SciPy-bundle 2020.11, SentencePiece 0.1.94, StringTie 2.1.4,
SuperLU 5.2.2, scikit-learn 0.23.2, snakemake 5.26.1, tqdm 4.51.0, vsc-mympirun 5.2.5, x264 20201026
- minor enhancements, including:
- add extension to R-bundle-Bioconductor 3.11: snpStats (#11586), SCANVIS (#11638)
- add extensions to R 4.0.0: coloc, Exact, lmom, gld, DescTools (#11587); nlsem (#11733); mitools, survey, tableone, jstable (#11841)
- add gxmapi extension (Python bindings) to GROMACS 2020.4 (#11640)
- add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs (#11654)
- enable NVPTX offload support in GCCcore 10.2.0 easyconfig (#11720)
- various bug fixes, including:
- prevent Minimac4 easyconfig from downloading libStatGen from GitHub (#7982)
- limit build parallelism for RAxML-NG to avoid build failure (#10363)
- fix source_urls in Geant4 easyconfigs (#11596)
- add alternate checksum for extensions in R easyconfigs: KernSmooth (#11600), codetools (#11616, #11736)
- fix BBMap version check in FusionCatcher v1.20 (#11608)
- add patch for TensorFlow 2.3.1 to fix installation on Arm64 (#11614)
- add patch for GCCcore 10.2 to fix __has_include regression (#11627)
- change default bitmaptype for IRkernel to cairo (#11645)
- set $JUPYTER_PATH to make Jupyter find the ipywidgets extension in recent IPython easyconfigs (#11649)
- add missing dependencies + fix moduleclass in CheckM easyconfigs (should be bio) (#11662)
- use Python 2 build dep for nodejs 12.19.0 (#11679)
- use correct OS deps in UCX (#11702)
- in-place update to magma 2.5.4 for PyTorch 1.2.0 (#11723)
- in-place update to magma 2.5.4 for PyTorch easyconfigs using fosscuda/2019b toolchain (#11726)
- add missing Java dep to Prokka (#11732)
- add patch to fix possible memory leak in OpenBLAS 0.3.3+ (#11745)
- do not treat warnings as errors in Java v1.8_191-b26-OpenJDK (POWER) (#11755)
- add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check (#11767)
- add missing gnuplot dependency in OpenFOAM easyconfigs (#11770, #11800)
- consistently add Java as a dep for prokka 1.14.5 (#11782)
- stick to http download URL in fetchMG easyconfig (https doesn't work) (#11788)
- other changes:
- rename XCfun to XCFun (#11603)
- rename ambiguous Ray easyconfigs to Ray-assembler and Ray-project (#11727)
- change 'rstudio' name to 'RStudio-Server' to agree with official name and better reflect what it provides (#11764)
- rename Sumo to SUMO for consistency (#11791)
v4.3.1 (October 29th 2020)
--------------------------
update/bugfix release
- added easyconfigs for 2 new toolchains:
- fosscuda/2020a (#11424) and intelcuda/2020a (#11425)
- added example easyconfig files for 75 new software packages:
- Bsoft (#6551, #11537), causallift (#11436), CAVIAR (#11158), CCfits (#11505), Cereal (#11506),
CFDEMcoupling (#6465), Check (#11295), chewBBACA (#11418), COMSOL (#11513), CUDAcore (#11295), Dalton (#5808),
DIRAC (#11414), ESMValTool (#6329), eSpeak-NG (#11236), ExifTool (#11521), FabIO (#11517), festival (#11236),
fetchMG (#11283), FHI-aims (#11198), Flexbar (#11305), FRUIT (#6613), FRUIT_processor (#6631), Gaussian (#4247),
GBprocesS (#11512), GDRCopy (#11295), Genome_Profiler (#6066), groff (#11200), ILAMB (#11309), kedro (#11436),
leidenalg (#11407), libav (#6194), libmo_unpack (#6329), libobjcryst (#11321), makeinfo (#11368),
mauveAligner (#11395), MBROLA (#11236), MDSplus-Java (#10705), MDSplus-Python (#10705), MyCC (#11283),
nanomax-analysis-utils (#11517), Nek5000 (#6408), NVHPC (#11391), OPERA-MS (#11410), ORFfinder (#7031),
phonemizer (#11236), Pingouin (#11280), Pint (#11151), pydantic (#11151), pyobjcryst (#11321), PyOpenCL (#11517),
pyspoa (#11438), QtPy (#11517), Qtconsole (#11517), rasterio (#11468), rasterstats (#11468), ReMatCh (#6067),
Ruby-Tk (#6613), SBCL (#11413), scikit-uplift (#11432), SDL (#6202), SDL2 (#6203), SDL2_image (#6203),
SDL_image (#6202), SeqKit (#11538), silx (#11517), SiNVICT (#11404), sonic (#11236), speech_tools (#11236),
Statistics-R (#11274), SUMO (#11435), tidybayes (#11335), treatSens (#11431), tsne (#11283), wandb (#11450),
WisecondorX (#11399)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2,
cURL 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0,
HMMER 3.3.1, Horovod 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 1.1.0, JupyterLab 2.2.8,
LLVM 11.0.0, libarchive 3.4.3, libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 1.3.2, libunwind 1.4.0,
libxcb 1.13, MAFFT 7.471, MDSplus 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3,
medaka 1.1.3, mpifileutils 0.10.1, NASM 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 2.7.7,
nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0,
PyGEOS 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, Python 3.8.6, pandas 1.1.2,
phonopy 2.7.1, picard 2.22.1, pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, ReFrame 3.2. re2c 2.0.3,
SAMtools 1.11, SCons 4.0.1, SQLite 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, spglib-python 1.16.0,
spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, torchvision 0.7.0,
UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc mympirun 5.2.0 X11 20201008, XGBoost 1.2.0,
XZ 5.2.5, Xerces-C++ 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5
- minor enhancements, including:
- use more EasyBuild installed dependencies for TensorFlow 2.2.0 (#11224)
- add additional extensions to R 4.0.0 easyconfig (#11340, #11430, #11487)
- add additional extensions to Bioconductor 3.11 bundle (#11341, #11488)
- make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (#11355)
- add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (#11387, #11568)
- build LibTIFF with -fPIC (#11527)
- update Java/1.8 wrapper to also support aarch64 (#11545)
- various bug fixes, including:
- add Python 3 as build dep for Xvfb 1.20.8 easyconfigs (#10745)
- patch out bug in collective primitive in TensorFlow 2.2.0 (#11175)
- add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (#11200)
- add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (#11273)
- add libtirpc as a build dep for HDF to fix installation on RHEL8 (#11279)
- fix build problems with make 4.2.1 on RHEL8 (#11282, #11371)
- change $LIBS in Ghostscript 9.27 easyconfig to include location of zlib library to link with (#11291)
- remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (#11307)
- make sure correct zlib is used in recent Ghostscript easyconfigs (#11319)
- remove GLog and GFlags from PyTorch 1.2.0 (#11327), 1.3.1 (#11325), 1.4.0 (#11322) and 1.6.0 (#11323)
- use PyTorch easyblock for PyTorch 1.3.1 (#11325)
- add missing git build dependency for OpenImageIO 2.0.12 (#11328)
- fix HDF 4.2.14 easyconfigs for RHEL8 (#11330)
- add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems (#11334)
- fix dependency on Bowtie of v0.x in seq2HLA easyconfigs (#11339)
- fix installation of Hadoop v2.10.0 on RHEL8 (#11358)
- add patch to fix installation of Sailfish v0.10.1 on RHEL8 (#11364)
- add patch to fix installation of FuSeq v1.1.2 on RHEL8 (#11365)
- fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (#11385, #11386)
- add patch for LAME configure script to make it check for correct ncurses symbol (#11388)
- add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (#11390)
- fix Multiwfn 3.6 installation on RHEL8 (#11402)
- fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 (#11409)
- fix broken worker easyconfigs (#11412)
- add ncurses runtime dependency to Clang easyconfigs (#11415, #11416, #11419, #11472)
- fix installation of Bioconductor 3.11 bundle on aarch64 (#11417)
- add patch to libunwind fixing a failure on POWER (#11421)
- fix infinite loop build bug on ppc64le for R 4.0.0 (#11428)
- fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (#11434)
- fix PyVCF easyconfig, only supports Python 2 (#11437)
- add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS (#11443, #11444, #11445)
- add missing DB dependency (required for DB_File) to easyconfigs for Perl (#11451, #11452)
- fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (#11453)
- use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (#11454)
- add missing UnZip dependency for Python 3.8.2 (#11458)
- add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (#11464)
- allow Kent_tools to build when MySQL installed at the OS level (#11471)
- add missing moduleclass to easyconfigs for:
- Arlequin 3.5.2.2 (#11473), MEGAHIT 1.2.8 (#11474) and 1.2.9 (#11475), PyCUDA 2019.1.2 (#11476)
- fix source for SQLite 3.31.1 (#11483)
- fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 (#11498)
- fix checksum in NAMD 2.12 easyconfigs + add source URL (#11515)
- add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (#11523)
- backport fixes for Score-P v6.0 (#11540)
- add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (#11561)
- add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 (#11575)
- other changes:
- update README on constructing source file for MATLAB (#6341)
- remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (#11301)
- make CI error messages less confusing ("is" -> "should be") (#11314)
- remove extentions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (#11429)
- cache M4 source tarball to avoid test failures because of download problems (#11469)
- rename jupyterhub to JupyterHub (#11571)
v4.3.0 (September 13th 2020)
----------------------------
feature release
- added easyconfigs for 2 new toolchains:
- gomkl/2020a and iomkl/2020a (#11036)
- added example easyconfig files for 49 new software packages:
- almosthere (#11152), arcasHLA (#10867), BioPP (#11113), Bracken (#10829), BUFRLIB (#11140), Calib (#11111),
CellRanger-ATAC (#11186), edlib (#10470, #11246), flatbuffers (#11109), gengetopt (#11117), graphite2 (#11168),
HeFFTe (#10990), hierfstat (#11249), immunedeconv (#11136), ioapi (#10959), itpp (#10958), LiBis (#11059),
libosmium (#11024), limix-bgen (#11152), minibar (#10470, #11246), misha (#11127), MOABS (#10747), moonjit (#11163),
NGLess (#11128), nsync (#11109), openCARP (#11117), OpenForceField (#11048), OpenMMTools (#11046), OpenMS (#10994),
PennCNV (#10986), plantcv (#10968), PlasmaPy (#10732), Portcullis (#11038), PycURL (#11169), PyGEOS (#11110),
pySCENIC (#11115), Reapr (#9296), RnBeads (#11142), sf (#11248), SLiM (#11172), stars (#11215, #11248), Sumo (#11071),
Telescope (#10943), tensorflow-probability (#10312), texlive (#11168), tidymodels (#11010), Trycycler (#11207),
umi4cPackage (#11127), variant_tools (#11169)
- added additional easyconfigs for various supported software packages, including:
- Bazel 3.4.1, Bonito 0.2.2, binutils 2.35, CP2K 7.1, Clang 10.0.1, ccache 3.7.11, ctffind 4.1.14, datamash 1.5,
ELPA 2020.05.001, Emacs 26.3, Flye 2.8.1, GCC(core) 10.2.0, googletest 1.10.0, HDF 4.2.15, Horovod 0.19.5,
imageio 2.9.0, JUBE 2.4.0, Julia 1.5.1, Kent_tools 401, Libint 2.6.0, libxsmm 1.16.1, MDSplus 7.96.8,
MDTraj 1.9.4, MariaDB 10.4.13, Meson 0.55.1, MotionCor2 1.3.2, NAMD 2.14, NCO 4.9.3, OpenFOAM 8, OpenMPI 4.0.5,
OptiX 6.5.0, Pandoc 2.10, Perl 5.32.0, PostgreSQL 12.4, PyCUDA 2019.1.2, PyFR 1.9.0, PyTorch 1.6.0,
PyZMQ 18.1.1, patchelf 0.12, pocl 1.5, pycocotools 2.0.1, pyproj 2.6.1.post1, QuantumESPRESSO 6.6,
RDKit 2020.03.3, rgdal 1.5, Salmon 1.3.0, Spark 3.0.0, scikit-image 0.17.1, scipy 1.4.1, snpEff 5.0,
sympy 1.6.2, TINKER 8.7.2, tqdm 4.47.0, Unicycler 0.4.8, VMD 1.9.4a43
- minor enhancements, including:
- also build Python libraries for ParaView 5.8.0 (#10927)
- add extensions to recent Bioconductor easyconfigs: FlowSorted.Blood.EPIC (#11021), DRIMSeq + stageR (#11053)
- add extensions to recent R easyconfigs: AICcmodavg + biomod2 (#11030), qqman (#11052), poLCA (#11081), coxed
(#11094), testit + data.tree (#11135), celestial + fasterize (#11206)
- add Config::Simple extension to Perl 5.30.x easyconfigs (#11051)
- update TensorFlow v2.1.0 (#11109) and v2.0.0 (#11233) easyconfigs to provide more dependencies via EasyBuild
- add CUDA compute capabilities to torchvision-0.5.0 (#11241)
- various bug fixes, including:
- patch to fix exporting images with PyQtGraph v0.10.0 (#10848)
- add missing Python dependency to PETSc 3.11.1 (#10907) and PETSc 3.12.x (#10908) easyconfigs
- use CMakeMake easyblock for installing magma to avoid C++11 related failures on POWER (#10929)
- fix source URL for Graphviz v2.40.1 (#10944)
- fix lapack.h for use with C++ in OpenBLAS 0.3.9 easyconfigs (#10960)
- add missing build dep on M4 for 2019b versions of netCDF-Fortran (#10972)
- update easyconfig for PyTorch 1.4 to use custom easyblock and run on POWER (#11000)
- create symlinks to incorrectly named directories in OpenBabel-3.1.1 so $BABEL_LIBDIR and $BABEL_DATADIR work properly (#11004)
- add missing Python build dep to recent ELPA easyconfigs (#11011)
- use is_generic_easyblock from filetools in easyconfigs test suite (#11020)
- fix sources in Portcullis v1.2.2 easyconfigs (#11038)
- add patch for FFTW 3.3.8 to avoid use of -no-gcc when building with Intel compilers, to fix installation on CentOS 8 (cfr. #10932) (#11050)
- add missing Python build dep for BEDTools 2.29.x (#11054)
- add missing SciPy-bundle and Kent_tools (for bedPartition command) dependencies to FLAIR (#11057)
- add patch to fix bug in LiBiS v20200428 easyconfig (#11059)
- use FFTW provided via EasyBuild for ScaFaCoS (#11060)
- fix undefined reference to 'qfloat16::mantissatable' in Qt5.14.1 (#11063)
- add alternative checksum for rstantools 2.0.0 extension (#11081)
- update checksums for R 3.6.0 packages and add patch for ppc (#11088)
- install scikit-learn 0.23.1 as a bundle and include required threadpoolctl extension (#11089)
- update pybind11 easyconfigs to use custom easyblock to install with pip (#11091)
- add recent six as extension to archspec installed on top of Python 3.7.4 (#11092)
- add missing Seaborn dependency to LiBis easyconfig (#11095)
- add missing dependencies for OpenPIV + switch to PythonBundle easyblock and include progressbar2 as extension (#11096)
- add missing argparse dep to TEtranscripts easyconfig (#11097)
- add missing pkg-config build dep in Octave 5.1.0 easyconfigs (#11100)
- don't statically link MUSCLE, to avoid requiring that glibc-static is installed in OS (#11102)
- add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs (#11104)
- add patch to h5py 2.8.0 (#11119) and 2.9.0 (#11118) easyconfigs to avoid MPI_Init on 'import h5py'
- add patch to support libbfd 2.34 API change in Score-P 6.0 (#11123)
- use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (#11143, #11260)
- add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with foss*/2019b toolchain (#11156)
- add missing pocl dependency in R 3.6.0 (#11157)
- update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix aggressive RPATH stripping (#11178)
- disable generating of man pages in recent libdrm easyconfigs to avoid installation failure if docbook-xsl is not installed (#11182)
- add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with --rpath (#11183)
- fix failing 'make check' for MPFR 4.x (#11187) and GMP (#11188) when installing with 'eb --rpath'
- add pkg-config as a build dependency for libglvnd (#11189)
- add missing libiconv build dep in recent Doxygen easyconfigs (#11191, #11257)
- enhance Java/11 wrapper to also support for aarch64/Arm (#11192)
- add pkg-config as a build dependency to Ghostscript 9.52, needed on aarch64/arm (#11194)
- add patch for pycrypto extension in recent Python easyconfigs to remove hardcoded /usr/include which causes problems when 'eb --sysroot' is used (#11202)
- fix installation of R v3.6.3 and v4.0.0 with foss/2020a on Arm (aarch64) (#11213)
- update PyTorch 1.4 easyconfigs to use custom easyblock (and do less downloading during installations) (#11219)
- other changes:
- don't require custom sanity_check_paths for 'CUDA' bundle easyconfigs (#10936)
- move intervaltree and sortedcontainers to main Python easyconfigs (#10969, #10970)
- disable qtwayland in Qt5 v5.14.1 (#11107)
- remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 easyconfigs (#11019)
- use pip to install h5py 2.10.0 (#11044)
- stop testing easyconfig PRs with Travis, only use GitHub Actions from now on (#11008, #11055)
- switch to Kent_tools built from source as dep for FusionCatcher (#11057)
- fall back to using PR target branch when determining "merge base" between PR branch & target branch fails in test suite (#11069)
- rename gtest to googletest (#11082)
- rename sdsl-lite to SDSL (to use one single name) (#11084)
- stop using 'remove_usr_bin'-patch in TensorFlow easyconfig, no longer required with updated TensorFlow easyblock (#11087)
- extend timeout for libxc-4.3.4 to avoid failing tests (#11126)
- move GitHub Actions status badge to top of README (#11138)
- fix code style issues in test (#11146)
- enable Flake8 on CI and fix issues (#11147)
- prefer gc GitHub site for source downloads (#11208)
- prefer https over ftp in source_urls of IgBLAST easyconfig (#11244)
v4.2.2 (July 8th 2020)
----------------------
update/bugfix release
- added easyconfigs for 2 new toolchains:
- golf/2020a (#10672)
- intel/2020.06, based on intel/2020a but with impi 2018 update 5 (#10864)
- added example easyconfig files for 36 new software packages:
- AmrPlusPlus (#9919), arrow (#10882), attrdict (#10827), Cartopy (#10685), dm-tree (#10775), dotNET-SDK (#10661),
FLAIR (#10860), fastqsplitter (#10706), GLFW (#10709), git-extras (#10440), hl7apy (#10728), hyperopt (#10735),
IgBLAST (#10889), IntelDAAL (#9848), ichorCNA (#10595), MARS (#10691), MITObim (#10897), MUST (#10849),
mhcnuggets (#9743), PAUP (#10830), Percolator (#10665), PyBerny (#10885), poetry (#10884), pycocotools (#10806),
python-hl7 (#10673), SHAPEIT4 (#10814), SYMPHONY (#10058), SunPy (#10676), sdsl-lite (#10691),
TEtranscripts (#10909, #10921), Tombo (#10646), tensorboardX (#10774), Unidecode (#10828), WHAM (#10736), XALT (#9792),
Xvfb (#10512)
- added additional easyconfigs for various supported software packages, including:
- Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, Blitz++ 1.0.2,
Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10,
dask 2.18.1, Elk 6.3.2, GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6,
geopandas 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0,
IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, MATIO 1.5.17,
MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 2.10.5, NiBabel 3.1.0,
Nipype 1.4.2, ncbi-vdb 20.10.7, numba 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006,
PDT 3.25.1, PRSice 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2,
Pysam 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1,
ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 1.3.959,
SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, Seaborn 0.10.1,
Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, StringTie 2.1.3, scikit-allel 1.2.1,
scikit-learn 0.23.1, snpEff 4.3t, Valgrind 3.16.1, VarScan 2.4.4,
vsc-mympirun 5.1.0, WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0
- minor enhancements, including:
- add extensions to R 4.0.0 easyconfig: drgee + stdReg (#10833), copCAR (#10911), ngspatial (#10913), drugCombo (#10914)
- add extensions to R-bundle-Bioconductor 3.11 easyconfig: BSgenome.Cfamiliaris.UCSC.canFam3 (#10840), SingleR (#10904)
- include extra extension and support for MPI in MAFFT v7.453 and v7.470 (#10853)
- add Array::Transpose to Perl (#10878)
- various bug fixes, including:
- fix dependencies and configuration of CoinUtils ecosystem (#10450)
- fix Togl configure patch so that it completely ignores TCL_SRC_DIR and TK_SRC_DIR (#10662)
- change Xerces-C++ to official CMakeMake build (fixes missing links to curl) (#10664)
- add -fPIC to toolchainopts in easyconfig for Lua 5.3.5 with system toolchain (#10671)
- remove hardcoded X86 target in LLVM easyconfigs (#10677)
- switch to https homepage and source_urls in libGLU easyconfigs (#10686)
- add patch for h5py 2.10.0 to avoid triggering MPI_Init at import (#10687)
- add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (#10692)
- update UDUNITS source_urls to https sources (#10693)
- add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (#10695, #10697)
- add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (#10710)
- add M4 builddependency to SuiteSparse 2019b easyconfigs (#10720)
- make sure WHAM is built with correct compiler (#10736)
- define MAX_JOBS in easyconfigs of PyTorch from v1.1.0 to v1.4.0 (#10772)
- add dm-tree and lz4 as dependencies to Ray v0.8.4 (#10775)
- fix source URL in recent ant easyconfigs (#10790)
- bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in Bioconductor 3.11 bundle, since sources for old versions have disappeared (#10791)
- add patch to Armadillo easyconfigs using the foss toolchain to prevent it from picking up MKL if installed system-wide (#10812)
- add missing kerneltree extension in FLAIR easyconfig (#10860)
- fix source URLs in Eigen 3.2.* (#10872) and 3.3.* (#10869) easyconfigs
- refer to issue in GitHub repo in configparser patch, since Bitbucket repo is disappearing (#10873)
- switch to github.com source URL for MetaPhlAn (#10874)
- switch to GitHub sources for ScientificPython 2.9.4 (#10875)
- switch to GitHub source URL for HPDBSCAN (#10876)
- download x265 3.2/3.3 sources from bitbucket.org/multicoreware/x265_git (#10905)
- fix download URL for libatomic in gc 7.6.12 easyconfigs (#10915)
- fix sanity_check_paths in CFITSIO-3.48-GCCcore-9.3.0.eb easyconfig (#10917)
- add missing dependencies for geopandas 0.7.0 (#10923)
- other changes:
- rename OpenPyXL 2.6.4 easyconfig to openpyxl (#10916)
v4.2.1 (May 20th 2020)
----------------------
update/bugfix release
- added easyconfigs for new common toolchains: foss/2020a (#10483, #10492), intel/2020a (#10494)
- added example easyconfig files for 66 new software packages:
- Alpha (#9994), antiSMASH (#10589), Arlequin (#10620), artic-ncov2019 (#10459), augur (#10405), AutoMap (#10419),
Bio-EUtilities (#10037), CaSpER (#10593), cdbfasta (#10547), cddlib (#10429), CoCoALib (#10429)
dftd3-lib (#10351), DoubletFinder (#10603), E-ANTIC (#10429), FastViromeExplorer (#10571), FIX (#8870),
FusionCatcher (#10134), geopandas (#10322), goalign (#10469), gotree (#10459), gretl (#10413), harmony (#10604),
HDF-EOS (#10534), HDF-EOS5 (#10536), HMMER2 (#10588), HyPo (#10642), king (#10365), libdeflate (#10459),
libfabric (#10616), libgit2 (#10453), libuv (#10444), mbuffer (#10524), MDAnalysis (#10545), MEM (#10605),
MESS (#10597), metaerg (#10037), MinCED (#10037), MitoZ (#7735), nauty (#10429), nifti2dicom (#10598),
NLMpy (#10029), ntCard (#10502), NTL (#10431), pIRS (#10508), popscle (#10550), ProtHint (#10549),
protozero (#10495), pysndfx (#10452), PyVCF (#10564), PyWavelets (#10501), rampart (#10459), rickflow (#10641),
RNA-Bloom (#10502), root_numpy (#10424), rstudio (#10619), ScaFaCoS (#10537), Scythe (#10524), SDSL (#10642),
SHAP (#10379), SNPomatic (#10524), SoX (#10452), swissknife (#10037),) Taiyaki (#10573), TCLAP (#10598),
torchaudio (#10516), wtdbg2 (#10524)
- added additional easyconfigs for various supported software packages, including:
- ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4,
CPLEX 12.10, CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 2.17.0, expat 2.2.9, FFmpeg 4.2.2,
FriBidi 1.0.9, GATK 4.1.5.0, GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 6.2.0, GROMACS 2020.1,
GTK+ 3.24.17, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2,
gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1,
IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1,
libarchive 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 2.0.4, librsvg 2.48.4, libsigsegv 2.12,
lrslib 7.0a, MEME 5.1.1, MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 1.3.1, MultiQC 1.8,
matplotlib 3.2.1, NGS-Python-2.10.4, NGS 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1,
Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1,
OpenMPI 4.0.3, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PLUMED 2.6.0, PMIx 3.1.5,
PROJ 7.0.0, Perl 5.30.2, Pillow 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 5.14.1,
R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3,
rioxarray 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 2.0.10, SIONlib 1.7.6, SQLite 3.31.1,
SRA-Toolkit 2.10.4, Salmon 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, StringTie 2.1.1,
SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2,
tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12,
wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, zstd 1.4.4
- minor enhancements, including:
- add additional extensions for recent versions of R (#10359, #10585, #10586, #10621) and R-bundle-Bioconductor (#10585, #10596, #10621)
- add additional extensions for recent versions of Perl (#10412, #10546, #10623)
- include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(#10458)
- include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (#10464)
- add alternate checksum for EMBOSS (#10607)
- various bug fixes, including:
- fix incorrect checksums for Amber patches (#8870)
- add patches to fix installation of R 3.6.2 on POWER (#9830)
- add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380)
- add Perl as a build dependency for recent Autoconf/Automake easyconfigs (#10408, #10426)
- fix source_urls in ICU easyconfigs (#10417)
- disable USER-INTEL package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (#10418)
- fix undefined reference to 'qfloat16::mantissatable' in Qt5-5.13.1-GCCcore-8.3.0 (#10425)
- get rid of double '-' in versionsuffix of torchtext easyconfig (#10472)
- fix broken Mako easyconfigs (#10480, #10627)
- move builddependencies to dependencies in OTF2 and Score-P easyconfigs (#10496)
- add missing cURL dep for LAMMPS (#10527)
- add Python 2 build dependency for OpenPGM (#10539)
- use OS_PKG_IBVERBS_DEV constant for OS dependency in PyTorch 1.4.0 easyconfigs (#10540)
- add missing Bison build dep in Graphviz easyconfigs (#10541)
- use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (#10559)
- add missing PyVCF dependency for BAMSurgeon (#10564)
- remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (#10565)
- fix ITK v5.0.1 easyconfig w.r.t. locale and location of libjpeg-turbo library (#10592)
- add patch to fix missing const qualifiers for ncurses (#10606)
- fix OS dependency for rstudio for Debian-based systems (#10608)
- fix Rmath paths in easyconfig for FastQTL v2.184 (#10612)
- add symlink for Arlequin commands + fix sanity check commands (#10620)
- fix recent binutils easyconfigs usign system toolchain for Fedora 32 / GCC 10 (#10633)
- replace '/path/to' with actual installation prefix in FuSeq scripts (#10640)
- other changes:
- check sdist with different Python versions in CI (#10388)
- use Bison 3.3.2 as build dep for flex 2.6.4 (#10403)
- mention http:// Pfam website rather than ftp:// in load message of BiG-SCAPE easyconfig (#10439)
- archive old Singularity configs (#10591)
- Singularity is not well suited to install via EasyBuild because it requires admin privileges to enable setuid
- stop using old hpcugent URL for cloning framework/easyblocks repos in CI (#10635)
- use SYSTEM constant for toolchain in easyconfigs already use 'system' toolchain (#10638)
v4.2.0 (April 14th 2020)
------------------------
feature release
- added example easyconfig files for 114 new software packages:
- ABRA2 (#10272), ABRicate (#10310), ADIOS (#10036), aNCI (#9929), any2fasta (#10310), apex (#10269),
archspec (#9898), ArviZ (#10366), autopep8 (#9626), BAMSurgeon (#10330), BatMeth2 (#10323),
BiG-SCAPE (#10352), BinSanity (#10001), Bonito (#10269), BSMAPz (#10283), BSseeker2 (#10039),
BUStools (#9838), Cbc (#10052), Cgl (#10048), CGmapTools (#10288), Clp (#10033), CoinUtils (#9937),
dtcwt (#9695), ELSI (#9857), EnsEMBLCoreAPI (#8734), fastq-pair (#9894), FigureGen (#10076), Fiona (#10321),
FuSeq (#10004), GenomeTools (#9797), GraphMap2 (#10299), GRASP (#9896), Groovy (#9809), gsport (#9821),
gubbins (#9689), igv-reports (#9977), inferCNV (#9686), iVar (#10291), joypy (#10212), JupyterLab (#9752),
kma (#10259), LAMMPS (#10371), lancet (#10271), libBigWig (#10006), libGridXC (#9858), libPSML (#5859),
LtrDetector (#10343), manta (#5104), medImgProc (#10228), MedPy (#9748), Mini-XML (#10036), mkl_fft (#9887),
Monocle3 (#9825), MoreRONN (#10255), motionSegmentation (#10228), NanoComp (#10212), NanoFilt (#10212),
nanoget (#10212), nanomath (#10212), NanoPlot (#10212), ngspice (#9922), ntEdit (#9836), ntHits (#9833),
occt (#9939), OCNet (#9955), OpenAI-Gym (#10347), OpenPIV (#9959), OpenPyXL (#10115), orca (#9518),
Osi (#10361), PartitionFinder (#9983), pauvre (#10212), polymake (#9904), pretty-yaml (#10041)),
PRSice (#9988), pycodestyle (#9626), pydot (#9899), pygraphviz (#9969), pylift (#10051), PyMC3 (#10279),
pyparsing (#9983), PyRe (#10095), python-weka-wrapper3 (#9704), PyTorch-Geometric (#9995), qcat (#10244),
RAxML-NG (#9990), Ray (#10302), rclone (#7934), Red (#9856), rstanarm (#9964), scikit-build (#9762),
scVelo (#9805), SECAPR (#9721), segmentation-models (#10211), SentencePiece (#10192), SEPP (#10047),
Shapely (#10309), Singular (#10030), SLATEC (#7529), spatialreg (#9767), split-seq (#9749), spoa (#9705),
SSN (#9955), STEAK (#10337), stpipeline (#9736), SVG (#9905), Togl (#9868), torchtext (#10193),
units (#9682), UQTk (#10279), WildMagic (#10044), Winnowmap (#10005), xtb (#9993), Zip (#9972)
- added additional easyconfigs for various supported software packages, including:
- ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34,
CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8,
DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1,
GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020,
GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1,
gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1,
Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166,
ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045,
LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453,
MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0,
Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1,
Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11,
PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1,
pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3
Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0,
SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0,
SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0,
TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2,
tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4,
- minor enhancements, including:
- add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (#9371)
- add additional extensions for R: HiddenMarkov (#9685), lmerTest (#9853), VSURF + Rborist (#10355)
- change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (#9764)
- build shared libs and install header files for Ghostscript (#9785)
- add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, #9891)
- add Perl extensions: Term::ReadLine::Gnu (#9901), URI::Escape and Set::IntervalTree (#10049)
- add dat directory to aNCI (#9929)
- add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (#10045)
- build SUNDIALS with 'pic' (#10278)
- add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (#10298)
- fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (#10367)
- update Java/1.8 wrapper to Java/1.8.0_241.eb (#10305)
- various bug fixes, including:
- use CMake for building double-conversion (#9659)
- update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (#9694)
- add alternate checksum for OpenMolcas 18.09 (#9701)
- use Github to download releases for MariaDB-connector-c (#9702)
- add -DOMPI_SKIP_MPICXX in configopts for MathGL, to avoid using mpicxx during build (#9703)
- make installing independent of build folder in pybind11 easyconfig (#9738)
- add Lua as a dependency to gnuplot (#9773)
- stick to http:// source URLS for ISL in GCCcore easyconfigs, since https:// doesn't work (#9784)
- add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (#9789)
- add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (#9865)
- revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (#9866)
- fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (#9867)
- add missing sanity_check_commands to cutadapt v1.18 and v2.7 easyconfigs (#9869)
- don't overwrite configopts in BLAST+ easyconfigs, append to it (#9875)
- add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, #10382)
- fix redefining of preconfigopts in OpenCV easyconfigs (#9895)
- use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (#9912)
- fix NCIPLOT build flags (#9915)
- add missing patch to iccifort libxc easyconfigs (#9918)
- use checkout@v2 in GitHub Actions to fix broken re-triggered tests (#9925)
- re-enable building utils in Siesta 4.1-MaX-1.0 release (#9936)
- fix homepage and source URLs in SLEPc easyconfigs by using https (#9943)
- fix source URLs for rgeos after source tarball was moved to CRAN archive (#9954)
- add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (#9957)
- patch GCC lisanitizer for glibc 2.31 (#9966)
- add Zip as build dependency for recent Bazel versions (#9972)
- fix checksums in Jellyfish v2.3.0 easyconfigs (#9997)
- fix source URLs for ParMGridGen easyconfigs (#10019)
- disable unintended Octave support in all libsndfile easyconfigs (#10027)
- fix sources for LS-PrePost 4.6 (#10236)
- security update for vsc-mympirun 4.1.9 (#10185)
- configure libwebp to also install libwebpmux (#10274)
- ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (#10326)
- fix undefined reference error due to libxc 4.3.4 built with CMake (#10356)
- fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (#10361)
- update checksums and homepage in tbb easyconfigs (#10285)
- other changes:
- use new custom easyblock in recent CMake easyconfigs (#9871, #9923)
- add check for redefined easyconfig parameters in easyconfig tests (#9876)
- use M4-1.4.18.eb for test installation in easyconfigs test suite (#9926)
- use https in homepage/source_urls of zlib-1.2.11.eb (#10018)
- add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (#10083)
- add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (#10237)
- add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (#10276)
v4.1.1 (January 16th 2020)
--------------------------
update/bugfix release
- added example easyconfig files for 27 new software packages:
- Autoconf-archive (#9658), breseq (#9603), CrossMap (#9483), CSBDeep (#9560), CNT-ILP (#9323), cytoolz (#9453), Faber (#9553),
Fiji (#8748), GARLI (#9404), Globus-CLI (#9565), GtkSourceView (#9526), gradunwarp (#9648), gsettings-desktop-schemas (#9529),
HyPhy (#9405), horton (#7449), IGMPlot (#9438), LEMON (#9323), Meld (#9530), mhcflurry (#9554), NCIPLOT (#9419), ncl (#9632),
OpenSlide (#9499), openslide-python (#9499), pythran (#9488, #9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381)
- added additional easyconfigs for various supported software packages, including:
- Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2,
GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10,
lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13,
OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1,
pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0,
SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2,
WPS 4.1, WRF 4.1.3
- added easyconfigs for intel/2020.00 toolchain (#9575)
- minor enhancements, including:
- add POWER9 support to CUDA 10.1 easyconfigs (#9442)
- build CMake in parallel (#9543)
- use NCCL for GPU ops in Horovod 0.18.2 easyconfig (#9562)
- update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (#9585)
- various bug fixes, including:
- fix remote launch of broker and workers for SCOOP (#9366)
- fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388)
- add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain (#9424)
- add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (#9454)
- fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (#9455)
- fix CMake 3.15.3 build on Power (+ enable building in parallel) (#9469)
- fix source URLs in xorg-macros easyconfigs (#9477, #9578)
- add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (#9479)
- remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS in various easyconfigs (#9528, #9577, #9615)
- use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (#9546)
- fix lpsymphony extension for R-bundle-Bioconductor (#9548)
- add correct 'old-versions' source URL to all Mesa easyconfigs (#9569)
- add missing SHA256 checksums for Armadillo (#9572)
- also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS (#9579)
- add SSL OS dependencies for GDAL 3.0.0 (#9586)
- add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (#9587)
- patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (#9590)
- patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (#9591)
- fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (#9601)
- use absolute path for extraction to allow relocating the build dir for g2log-1.0 (#9604)
- add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (#9611)
- add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (#9621)
- update ctffind website (#9622)
- make sure we use easybuild Clang in pocl easyconfigs (#9624)
- make postinstallcmds independent of current working directory in OpenCV 3.1.0 easyconfigs (#9628)
- update source_urls to include old releases folder in libsodium easyconfigs (#9632)
- fix source URLs for ant v1.10.5 - v1.10.7 (#9633)
- update URLs to new location of libxc (#9635)
- add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (#9644)
- update source URLs in QCA 2.1.0 easyconfigs (#9647)
- fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI) (#9649)
- fix tesseract 4.1.0 dependencies (#9650)
- make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (#9652)
- use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters (#9657)
- fix pyfits easyconfig by adding missing d2to1 extension (#9687)
- other changes:
- disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492)
- require that sanity_pip_check is enabled in new/changed easyconfigs (#9516, #9576)
- update copyright statements for 2020 (#9598)
- allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (#9634)
v4.1.0 (December 4th 2019)
--------------------------
update/bugfix release
- added example easyconfig files for 46 new software packages:
- Amara (#9340), anvio (#9387), Arriba (#9226, #9244), attr (#7824), bibtexparser (#9284), bwa-meth (#9217), CITE-seq-Count (#9237),
CoordgenLibs (#9374), dtcmp (#9052), fatslim (#9193), GromacsWrapper (#9177), GULP (#9243), hdf5storage (#9195),
ITSTool (#7260), kim-api (#8786), kwant (#9238), libarchive (#9052), libcircle (#9052), libxml2-python (#7260),
lifelines (#9215), lwgrp (#9052), maeparser (#9374), MaxQuant (#9281), MethylDackel (#9216), MoviePy (#9205),
mpifileutils (#9052), mpiP (#9059), nanofilt (#8502), NOVOPlasty (#9326), openkim-models (#8786), parallel-fastq-dump (#9218),
pasta (#9348), pyqstem (#9277), python-Levenshtein (#9237), RapidJSON (#9373), RDFlib (#9346), RQGIS3 (#9125),
Short-Pair (#9376), SpliceMap (#9375), TRIQS-cthyb (#9230), TRIQS-dft_tools (#9230), TRIQS-tprf (#9230),
UMI-tools (#9237), VarDict (#7283), Xmipp (#9257), XSD (#9347)
- added additional easyconfigs for various supported software packages, including:
- awscli 1.16.290, BLIS 0.6.0, Bazel 1.1.0, Biopython 1.75, Blender 2.81, bokeh 1.4.0, CONCOCT 1.1.0, CUDA 10.2.89,
Catch2 2.11.0, CellRanger 3.1.0, CheckM 1.0.18, dask 2.8.0, deepTools 3.3.1, FastANI 1.2, Flye 2.6, GDCM 3.0.4,
GTDB-Tk 0.3.2, Glade 3.8.6, Hadoop 2.9.2, h5py 2.10.0, hypothesis 4.44.2, IPython 7.9.0, Kaiju 1.7.2, Kraken 1.1.1,
libsodium 1.0.18, MEGAHIT 1.2.8, Mesa 19.2.1, MetaBAT 2.14, matplotlib 3.1.1, metaWRAP 1.2.2,cNCCL 2.4.8,
NGS 2.10.0, NiBabel 2.5.1, netCDF 4.7.1, networkx 2.4, numba 0.46.0, OpenCV 3.4.7, OpenCoarrays 2.8.0, OpenEXR 2.4.0,
OpenFOAM v1906, OpenImageIO 2.0.12, ParaView 5.6.2, Pillow 6.2.1, PyTorch 1.3.1, PyYAML 5.1.2, Pysam 0.15.3,
picard 2.21.1, prokka 1.14.5, protobuf 3.10.0, R-keras 2.2.5.0, Racon 1.4.7, SCOTCH 6.0.9, SRPRISM 3.1.1,
Salmon 0.14.2, SciPy-bundle 2019.10, Subread 2.0.0, scikit-image 0.16.2, scikit-learn 0.21.3, TRIQS 2.2.1,
TensorFlow 1.15.0, TensorFlow 2.0.0 w/ fosscuda/2019b, Tkinter 3.7.4, ToFu 1.4.1, tbb 2019_U9, Xerces-C++ 3.2.2,
Xmipp 3.19.04, yaff 1.6.0
- added easyconfigs for intelcuda/2019b toolchain (#9271)
- minor enhancements, including:
- tweak Java 1.8 wrapper to use different Java version on POWER systems (#9081)
- add jupyter_nbextensions_configurator extension to IPython 7.7.0 easyconfigs (#9133)
- add additional extensions to R 3.6.0 easyconfigs (#9184, #9275)
- add additional extensions to R-bundle-Bioconductor 3.9 easyconfig (#9185, #9349, #9410)
- enhance sanity check in cutadapt 1.18 easyconfigs + consistently use PythonBundle & use_pip (#9219)
- update cuDNN 7.6.4.38 easyconfigs to support both x86_64 and ppc64le (#9331)
- tweak NCCL 2.4.8 easyconfig to support x86_64 and ppc64le (#9336)
- define $SPARK_HOME in generated module file for Spark 2.4.0 (#9408)
- add sanity check command for matplotlib 3.x with Python 3 to check import from mpl_toolkits (#9413, #9414)
- various bug fixes, including:
- explicitly set SYSCONFDIR configure option in TurboVNC easyconfig (#9137)
- patch pigz Makefile so zlib provided by EasyBuild is picked up (#9138)
- add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, to avoid picking up LibTIFF installed in system (#9146)
- add freetype as dependency to OpenImageIO, to avoid picking up freetype installed in system (#9147, #9152)
- fix definition of fosscuda/2019b to make sure it works with hierarchical MNS (#9178)
- add missing setuptools_scm extension required to build dateutil extension in Python 3.7.0 easyconfigs (#9209)
- add Python as build dependency for recent Bazel versions (#9223, #9299, #9342)
- fix homepage & description in Bioconductor easyconfigs (#9225)
- fix checksum in Stacks 2.41 easyconfig after sneaky re-release (#9232)
- apply fixes to ImageJ 1.51k easyconfig (#9245)
- consistently use patch for OpenCV 3.4.7 (#9279)
- use protobuf 3.10.0 as build dep for TensorFlow 2.0.0 w/ fosscuda/2019b + use nodocs variant of git as build dep (#9298)
- add Jasper dependency to Qt5 v.5.13.1 (#9313)
- fix Python 3.7.2 required OpenSSL version for old OS to the one provided on the same toolchain (#9324)
- add missing extensions required by Sphinx & pytest to easyconfigs for Python 3.7.2 and 3.7.4 (#9329)
- update TensorFlow v1.14.0 + v2.0.0 CUDA patch to handle compiler wrappers like ccache (#9333)
- patch binutils 2.31.1 and 2.32 to fix compatibility with RHEL8 (#9335)
- add missing extensions in TensorFlow 2.0.0 easyconfigs (+ update to tensorboard/tensorflow-estimator 2.0.1) (#9338)
- fix logic to determine location of scripts dir + ensure right compiler flags are used in KAT easyconfigs (#9360)
- add missing GCCcore-6.3.0_fix-sanitizer_linux.patch in GCCcore 6.4.0 easyconfig (#9362)
- fix linker errors when linking with libhts.a for MetaBAT 2.12.1 (#9379)
- add egg-info file via patch in VTK v8.2.0, for Pytho 2.7.15, 3.7.2, 3.7.4 (#9386)
- promote binutils to a runtime dependency for Python in GCCcore based builds (#9402)
- fix archive URL typo for ncdf4 (#9407)
- fix problems with mpl_toolkits namespace for matplotlib easyconfigs using Python 2 (#9415, #9416, #9417)
- other changes:
- ignore commented out lines in easyconfig files when checking for http:// URLs (#9224)
- add GitHub Actions workflow to run easybuild-easyconfigs test suite (#9231, #9255)
- archive old patches for Xmipp 3.1 (#9256)
- speed up easyconfigs test suite by avoiding re-parsing and re-ordering of easyconfigs (#9236)
- only run easyconfigs test suite with Python 2.7 & 3.6 + Lmod 7 in Travis CI (#9297)
- archive ACML easyconfigs (#9367)
- update CMake build in Eigen 3.3.7 to use more recent toolchain (#9398)
v4.0.1 (October 15th 2019)
--------------------------
update/bugfix release
- added example easyconfig files for 58 new software packages:
- ADOL-C (#9098), ALFA (#9106), ASTRID (#9088), Annif (#8536), bnpy (#8989), bpp-core (#9064), bpp-phyl (#9064),
bpp-seq (#9064), Clang-Python-bindings (#9084), CPB (#5869), Centrifuge (#8714), Chromaprint (#9047), Con3F (#8755),
DeepSurv (#8096), Essentia (#9054), FastRFS (#9088), GAT (#5871), Gaia (#9049), Gctf (#9097), GenomeMapper (#5872),
Infomap (#9091), kpcalg (#8740), libglvnd (#9111, #9130), libsamplerate (#9046), libssh (#8865), libzip (#9073),
MetaboAnalystR (#8773), Metaxa2 (#8939), MotionCor2 (#8942), NFFT (#9085), PhyML (#9103), PlaScope (#8714),
PyCharm (#9100), pbcopper (#8928), pbmm2 (#8929), phylokit (#9088), phylonaut (#9088), phyx (#9090), pycma (#8834),
Q6 (#9069), Qt5Webkit (#9120), ROME (#9050, #9062), rioxarray (#9007), SVDquest (#9088), savvy (#9124),
sciClone (#7806), shapAAR (#8983), shrinkwrap (#9124), Structure (#5866), trimAl (#9063), thurstonianIRT (#9080),
TurboVNC (#9110, #9111, #9128), Tracer (#8970), TagLib (#9048), TRIQS (#8835), THetA (#8875), vcfnp (#5862),
WebSocket++ (#8842)
- added additional easyconfigs for various supported software packages, including:
- Armadillo 9.700.2, arpack-ng 3.7.0, BLASR 5.3.3, Bazel 0.26.1 + Bazel 0.29.1, Cufflinks 20190706,
DL_POLY_Classic 1.10, FFmpeg 4.2.1, Go 1.13.1, Horovod 0.18.1, IOR 3.2.1, Julia 1.2.0, LLVM 9.0.0, Mesa 19.1.7,
Molden 6.1, Mono 6.4.0.198, NCO 4.8.1, , Net-core 3.0.0, Nim 1.0.0, OpenFOAM 2.2.x, PGI 19.7, PLUMED 2.5.2,
PMIx 3.1.4, PostgreSQL 11.3, psycopg2 2.8.3, QGIS 3.4.12, QScintilla 2.11.2, Qt5 5.13.1, ReFrame 2.19,
Rust 1.37.0, Spack 0.12.1, TAMkin 1.2.6, TensorFlow 1.14.0 w/ fosscuda/2019a, TensorFlow 2.0.0 w/ foss/2019a,
UCX 1.6.1, VEP 96.0, xarray 0.13.0
- added easyconfigs for fosscuda/2019a toolchain (#9066)
- minor enhancements, including:
- add EBImage extension to easyconfig for R-bundle-Bioconductor 3.9 (#8982)
- add check for http:// URLs in easyconfig files added/changed in PRs (#9012)
- add bbmle/emdbook/SOAR/rasterVis/tictoc extensions to R 3.6.0 easyconfigs (#9037)
- updated PyQt5 5.12.1 easyconfig to also build sip files + minor readability changes (#9071)
- enabled SQLITE_ENABLE_COLUMN_METADATA, which is needed for GDAL (and QGIS) (#9118)
- also install include/GL/internal/ for recent Mesa installations (#9129)
- various bug fixes, including:
- add ncurses as dependency to lftp (#8646)
- add patch for gettext 0.19.8* to avoid picking up global git config that could break the installation (#8957)
- fix source_urls in GlimmerHMM easyconfigs (#8980)
- add patch for PyTorch 1.2.0 to use version of torchvision that is compatible with PyTorch 1.2.0 (#8986)
- clarify the comment regarding the optarch setting in ITK-5.0.1 (#8991)
- fix homepage & description in easyconfig file for YAPS (#8993)
- add patch for PyTorch 1.2.0 to fix failing softmax test on Intel Sandy Bridge (#9010)
- fix permissions for TRF (#9034)
- ICU needs Python 2.7+ to build, so add that as builddependency (#9053)
- fix urls for Anaconda and Miniconda (#9087)
- use a cuDNN version that has support for the CUDA version in fosscuda/2019a (CUDA 10.1) in PyTorch, TensorFlow and Theano easyconfigs (#9112)
- other changes: