forked from easybuilders/easybuild-easyconfigs
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathRELEASE_NOTES
1657 lines (1511 loc) · 107 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 http://easybuild.readthedocs.org/en/latest/Release_notes.html.
The latest version of easybuild-easyconfig provides 8,831 easyconfig files, for 1,437 different software packages,
27 different (compiler) toolchains, 13 software bundles and 1 meta-package.
v3.6.0 (April 26th 2018)
------------------------
feature release
- added easyconfigs for new toolchain golf/2018a (#6080)
- added example easyconfig files for 39 new software packages:
- ARAGORN (#6138, #6219), amask (#6105), BamBam (#5490), Bandage (#6053), bcgTree (#6057), biobambam2 (#6040),
CODEX2 (#5972), coverage (#5964), DANPOS2 (#5870), EasyQC (#6175), elastix (#6074), FRANz (#6035), Filtlong (#6050),
FriBidi (#6181), Gblocks (#6057), Grace (#6036), LMfit (#6119), libmaus2 (#6040), MathGL (#6033),
MiGEC (#6047), MiXCR (#6045), Miniconda3 (#6075), Multiwfn (#5403), mosdepth (#6169), Nim (#6167),
Porechop (#6051), propy (#6091), Roary (#6056), Rtree (#6222), SALib (#6145), SMRT-Link (#6218), SimpleITK (#6172),
spectral.methods (#6104), supernova (#6193), TEToolkit (#5912), tbl2asn (#6139), udocker (#5770), vartools (#6102),
XCfun (#5975)
- added new easyconfigs for existing toolchains:
- gmpich/2017.08 (#6143), goolfc/2018a (#6129), intel/2018.02 (#6077), iomkl/2018.02 (#6088)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 8.6.3, Anaconda2 5.1.0, Anaconda3 5.1.0, binutils 2.30, dask 0.17.2, FFmpeg 4.0, GCC(core) 7.3.0
GROMACS 2016.5, olf 2018a.eb, HTSlib 1.8, LLVM 6.0.0, Mesa 17.3.6, netCDF 4.6.0, Octave 4.2.2, OpenCV 3.4.1,
PLUMED 2.4.1, PROJ 5.0.0, PostgreSQL 10.3, Qt5 5.10.1, R 3.4.4, SAMtools 1.8, Spack 0.11.2 TensorFlow 1.7.0,
VTK 8.1.0
- minor enhancements, including:
- add test to ensure there's only one variant for each dependency in dep graph of easyconfigs using particular toolchains (#5970, #6023)
- add extensions required by CODEX2 v20180227 to Bioconductor w/ R 3.4.3 (#5972)
- add config file for https://pre-commit.com/ (#5785)
- add custom sanity check paths for GraphicsMagick consistently (#5997)
- add custom sanity check paths to recent Ghostscript easyconfigs (#5998)
- add svd, Rssa, JBTools, RUnit, DistributionUtils and gapfill extensions for R 3.4.3 (#6099)
- add additional extensions to Bioconductor 3.6 bundle (#6136)
- add xlrd extension to recent Python 2.x and 3.x easyconfigs (#6162)
- minor changes, including:
- use gettext 0.19.8.1 on top of libxml2 2.9.7 as dep for git built with foss/2018a (#5993)
- bump hwloc dep for OpenMPI 2.1.2 that is part of iomkl/2018a to v1.11.8 (#5994)
- use non-interactive plotting backend by default for matplotlib 2.1.2 (#6024)
- don't use bare Perl as dependency for git with foss/2018a, use variant with extensions (#6058)
- various bug fixes, including:
- fix moduleclass & add custom sanity_check_paths in gettext easyconfigs (#5991)
- drop use of --disable-dlopen in (recent) OpenMPI easyconfigs due to negative performance impact (#6060)
- add missing XZ dep in Python 3.6.4 easyconfigs built with */2018a toolchain (#6065)
- add 10 packages that were previously downloaded in Python 3.6.4 easyconfigs (#6081)
- add patch for Tensorflow 1.6 & 1.7 to include missing -lrt link flag (needed in CentOS6) (#6089)
- fix checksums for R extensions that were updated in place in easyconfigs for R versions 3.4.3 & 3.4.4 (#6118)
- include pkg-config as build dep in recent R easyconfigs (required for atleast nloptr) (#6122)
- remove Intel-specific workaround for 'undefined symbol: __stack_chk_guard' issue from Python 3.6.4 foss/2018a easyconfig (#6130)
- add configopt --without-matlab/octave to all NLopt easyconfigs (#6132)
- also consider lib64 in sanity_check_paths for Bison 3.0.4 (#6170)
- don't use libyaml built with dummy as dep for PyYAML (#6208)
- add missing pkg-config build dep in recent GObject-Introspection, GLib & cairo easyconfigs (#6216)
- don't include (ancient version of) Time::HiRes as Perl extension, since it's a core Perl module (#6225)
- this fixes problems with the installation of BioPerl and proovread
- add missing XML-LibXML dependency in recent BioPerl easyconfigs (#6226)
- add --without-ada configure option in recent ncurses easyconfigs (#6228)
- add patch for snaphu to fix segmentation fault due to use of short integer (#6230)
v3.5.3 (March 7th 2018)
-----------------------
bugfix/update release
- added example easyconfig files for 2 new software packages:
- CNVkit and hmmlearn (#5954)
- added additional easyconfigs for various supported software packages, including:
- matplotlib 2.1.2, TensorFlow 1.6.0
- minor enhancements, including:
- re-enable testing against environment modules, bump Lmod to 7.7.16 (#5944)
- add cghFLasso extension to R 3.4.3 easyconfigs (#5953)
- add 'Math::CDF' extension to recent Perl modules (#5957)
- various bug fixes, including:
- add missing --enable-ld-version-script configure option for LibTIFF 4.0.9 built with GCCcore/6.4.0 (#5945)
- hard disable UCX support in recent OpenMPI versions, to dance around bug in OpenMPI configure script (#5949)
v3.5.2 (March 2nd 2018)
-----------------------
bugfix/update release
- added example easyconfig files for 24 new software packages:
- AMPL-MP (#5800), AmberTools (#5632), bcolz (#5864), detonate (#5709), dropEst (#5734), EvidentialGene (#5627),
faceswap (#5825), fineSTRUCTURE (#5663), Gradle (#5828), gbs2ploidy (#5877), HIPS (#5725), Ipopt (#5800),
libMemcached (#5804), MEGAHIT (#5748), Mmg (#5807), methylpy (#5874), pstoedit (#5884), python-igraph (#5905),
RNAcode (#5854), Seq-Gen (#5695), Stata (#5102), scikit-allel (#5864), TetGen (#5681), zarr (#5864)
- added new easyconfigs for existing toolchains: giolf/2018a (#5777), goolfc/2017b (#5768), iomkl/2018a (#5878)
- added additional easyconfigs for various supported software packages, including:
- CP2K 5.1, IPython 6.2.1, OpenFOAM v1712, Perl 5.26.1, Python 3.6.4, TensorFlow 1.5.0, X11 20180131
- minor enhancements, including:
- add feather and tidyverse as extensions for R 3.4.3 (#5693)
- build recent PLUMED versions with all modules enabled (#5696)
- add MAST/splatter/scDD to Bioconductor 3.6 bundle (#5704)
- add dummies as extensions for R 3.4.3 + monocle/scde/ROTS (+ deps) to Bioconductor 3.6 bundle (#5724)
- include io and statistics extensions to Octave 4.2.1 easyconfigs (#5798)
- switch to using TensorFlow as backend for recent versions of Keras (#5821)
- various bug fixes, including:
- using the correct binutils in jemalloc 5.0.1 easyconfig using GCCcore/6.4.0 (#5659)
- fix source URLs for MPC (#5662)
- add Tkinter as dependency for ASE & matplotlib using Python 3.6.3 (#5658)
- fix versions for updated extensions in Bioconductor 3.6 bundle (#5704, #5724, #5880)
- fix missing M4 build dependency in nettle (#5722)
- fix homepage for OpenFOAM 4.x & 5.x, should be openfoam.org (#5422, #5780)
- add matplotlib, cairo & PyCairo dependencies for graph-tool 2.26 + enhance sanity check (#5787)
- fix hardcoded version in scikit-image easyconfigs (#5822)
- fix pkgconfig moduleclass, 'data' doesn't make much sense (#5817)
- add sanity check in recent matplotlib easyconfigs to ensure that Tkinter is available (#5689, #5896)
- correct MPI path when building ABINIT with 'foss' toolchain (#5760)
- patch Hyperopt to make it work with networkx 2.0 (#5642)
- add Tkinter sanity check to ASE easyconfigs (#5691, #5909)
- include autotools as build dep in git easyconfigs (#5718)
- fix sanity check paths for Debian OS in JasPer easyconfigs (#5897)
- fix source_urls for recent versions of ABINIT (#5908)
- add patch for recent GDAL easyconfigs using intel toolchain to fix icc get stuck on compiling ceos.c (#5915)
- add explicit zlib dependency in Tkinter 2.x and 3.x (#5797, #5926)
- fix source URLs & homepage in Singularity easyconfigs (#5927)
- fix installation of TensorFlow 1.3 via binary wheel after introducing TensorFlow easyblock (#5938)
v3.5.1 (January 16th 2018)
--------------------------
bugfix/update release
- added easyconfigs for foss/2018a and intel/2018a common toolchains (#5577), (#5578)
- added example easyconfig files for 26 new software packages:
- BeautifulSoup (#5601), Calendrical (#5588), ChimPipe (#5560), crb-blast (#5124)), dammit (#5125), deepTools (#5536),
FastQ_Screen (#5404), FoX (#5496), GffCompare (#5581), GlimmerHMM (#5559), LocARNA (#5548), MapSplice (#5566),
MariaDB-connector-c (#5557), NextGenMap (#5430), nd2reader (#5545), PIMS (#5545), Pysolar (#5585), phono3py (#5551),
preseq (#5569), proovread (#5513), QUAST (#5610), RNA-SeQC (#5589), RNAclust (#5607), Ragout (#5608),
SOAPfuse (#5417), TransDecoder (#5125)
- added additional easyconfigs for various supported software packages, including:
- BLAST+ 2.7.1, BamTools 2.5.0, Boost 1.66.0, Clang 5.0.0, dask 0.16.0, FFmpeg 3.4.1, GROMACS 2016.4, HDF5 1.8.20,
matplotlib 2.1.1, PLUMED 2.4.0, Pillow 5.0.0, Qt5 5.9.3, QuantumESPRESSO 6.2, Ruby 2.5.0, Rust 1.22.1
- minor enhancements, including:
- include gomms in list of extensions for R 3.4.3 (#5547)
- clean up BamTools easyconfigs to rely on updated easyblock + add SHA256 checksums (#5575)
- add Time::HiRes to recent Perl versions (#5616)
- add DNAcopy & dupRadar extensions to bundle for Bioconductor 3.6 (#5587, #5618)
- switch to using install_target rather than now deprecated use_easy_install and use_setup_py_develop (#5625)
- various bug fixes, including:
- avoid auto-downloading of parcel in gdc-client 1.3.0 easyconfig (#5523)
- fix permissions on make_raw_alos.pl script in ROI_PAC installation (#5546)
- remove erroneous patch for Intel compiler support in Perl 5.26.0 easyconfig built with GCCcore/6.4.0 (#5561)
- include HWxtest as extension to fix issue with diveRsity in R 3.4.3 easyconfig file (#5570)
- add pkg-config as build dependency for fontconfig, harfbuzz, gnuplot, pango (#5580)
- fix versions of updated extensions in BioConductor bundle (#5587, #5618)
- add missing libpng dependency in ROOT 6.10.08 easyconfigs (#5595)
- fix option passed to configure in M4 (#5606)
- rename SIBELia to Sibelia (#5603)
- add patch for binutils 2.26 to fix compatibility with GCC 6.x (#5611)
- fix for dependencies was set twice in OpenMPI 3.0.0 easyconfig (#5619)
- fix download URL in comment of Kent tools easyconfigs (#5633)
- add SHA256 checksums to various easyconfigs (#5635, #5636, #5639)
- add rdma-core-devel to OS dependencies for OpenMPI 3.0.0 (#5648)
v3.5.0 (December 15th 2017)
---------------------------
feature release
- added example easyconfig files for 39 new software packages:
- AmberMini (#5476), arrow (#5416), bat (#5416), CIRCexplorer (#5356), CIRCexplorer2 (#5470), CIRI (#5358),
FALCON (#5265), FastaIndex (#5465), find_circ (#5348), future (#5236), GapCloser (#5465), glibc (#5428),
GRNBoost (#5373), HDFView (#5391), Horovod (#5239), HPDBSCAN (#5371), Hyperopt (#5455), IntelClusterChecker (#4970),
ITK (#5434), LAST (#5465), MDTraj (#5317), Meson (#5228), mkl-dnn (#5319, #5362), Ninja (#5228), OpenKIM-API (#5479),
ParmEd (#5476), PCRaster (#5386), piSvM (#5308), piSvM-JSC (#5316), PTESFinder (#5359), pybedtools (#5347),
pymbar (#5476), pyScaf (#5465), QIIME2 (#5355), QTLtools (#5361), Redundans (#5465), Rmath (#5361), sbt (#5373),
SNAP (#5465)
- added new easyconfigs for existing toolchains: intel/2017.09 (#5303), intel/2018.00 (#5129), intel/2018.01 (#5345)
- added additional easyconfigs for various supported software packages, including:
CGAL 4.11, CMake 3.10.0, Caffe 1.0, FFTW 3.3.7, GATE 8.0, gnuplot 5.2.2, HPCG 3.0, HTSlib 1.6, Keras 2.1.2,
LLVM 5.0.0, Mesa 17.2.5, mpi4py 3.0.0, netCDF 4.5.0, OpenFOAM 5.0, ParaView 5.4.1, R 3.4.3, Ruby 2.4.2, Rust 1.21.0,
SCons 3.0.1, Szip 2.1.1, Theano 1.0.0, VTK 8.0.1, X11 20171023
- minor enhancements, including:
- add SHA256 checksums to Autoconf (#5304), Automake (#5305), libtool (#5306) and M4 (#5307) easyconfigs
- avoid hardcoding extension versions in worker easyconfig, include 'perl' as OS dep (#5324)
- enable building ScaLAPACK in parallel with enhanced ScaLAPACK easyblock (#5331)
- include RInside extension in R 3.4.0 easyconfig (#5354)
- clean up configure options that are now handled by R easyblock (#5478, #5485)
- update Octave easyconfigs to use Octave easyblock, add extensions for latest Octave versions (#5484, #5503, #5507)
- add Log4perl extension to Perl 5.26.0 easyconfigs (#5511)
- various bug fixes, including:
- add missing extensions required by MultiQC & stick to networkx 1.11 (#5240)
- disable optarch when using intel compilers and enable tests in all libxc easyconfigs (#5256, #5257)
- avoid downloads when installing matplotlib 2.1.0 w/ Python 2.7.14 (#5267)
- fix $CPATH in recent libffi easyconfigs + enhance sanity check & add checksum (#5271)
- use Github source URL, run autogen.sh + include Autotools build dep for numactl (#5286, #5296, #5297, #5299, #5302)
- add hwloc to GROMACS dependencies (#5295)
- fix source_urls (& sources spec) for GATE (#5367)
- consistently add Autotools build dep in recent netCDF easyconfigs (#5394)
- fix check in test suite for binutils build dep when GCCcore used as toolchain (#5436)
- libdap 3.19.1 checksum changed (#5473)
- disable new rfkill feature in easyconfig for util-linux 2.31 since it requires a recent kernel (#5480)
- add missing PROJ dependency in recent GDAL easyconfigs (#5481)
- fix name in TensorFlow easyconfigs (was 'TensorFlow') (#5495)
- fix checksum for Szip 2.1.1 (#5517)
- fix order of extensions for FSLeyes, add missing MarkupSafe (dep for Jinja2) (#5520)
v3.4.1 (October 17th 2017)
--------------------------
bugfix/update release
- added easyconfigs for new toolchain giolf/2017b (#5140)
- added example easyconfig files for 13 new software packages:
- ASAP3 (#5200), Albacore (#5153), CatMAP (#5225), DLCpar (#5209), FSLeyes (#5192), IQ-TREE (#3695), NEST (#5515),
nanonet (#5149), OMA (#5211), oxford_asl (#5193), QEMU (#5220), REMORA (#5159), SAS (#5208), supermagic (#5187)
- added additional easyconfigs for various supported software packages, including:
- Anaconda2/3 4.4.0, Blender 2.79, Boost 1.65.1, CMake 3.9.4, FFmpeg 3.3.4, GCC 5.5.0, h5py 2.7.1, Keras 2.0.8,
matplotlib 2.1.0, mympingpong 0.8.0, OpenCV 3.3.0, OpenFOAM-Extend 4.0, OpenMPI 2.1.2 + 3.0.0, Pillow 4.3.0,
Python 2.7.14 + 3.6.2, SAMtools 1.6, scikit-image 0.13.0, scikit-learn 0.19.0, Tensorflow 1.3.0, vsc-mympirun 4.0.2
- minor enhancements, including:
- add xkeyboard-config component in X11 bundle (#5066)
- clean up use of wcleanAll in OpenFOAM-Extend easyconfigs, now handled by OpenFOAM easyblock (#5131)
- also install run_rcorrector.pl with Rcorrector (#5135)
- add SHA256 checksum to PyCUDA easyconfig (#5154)
- fix/improve description in HDF5 easyconfigs (#5182)
- include heatmap3 extension for R 3.4.0 (#5185)
- add ComplexHeatmap to Bioconductor 3.5 bundle + dep pkgs in R 3.4.0 easyconfig (#5195)
- various bug fixes, including:
- fix source URLs for AUGUSTUS 3.2.3 (#5119)
- fix building Bison 2.5 on systems with recent glibc (#5130)
- also consider rdma-core-devel as alternative to libibverbs-devel OS dependency (#5132)
- consistently use empty toolchain version in icc & ifort easyconfigs to ensure that GCC(core) dep is loaded during installation (#5133, #5134)
- add patches for Boost 1.64.0 to fix known issues (#5148)
- remove PyCUDA easyconfig for intel/2017a, doesn't work due to incompatibility between GCC 6.3.0 & CUDA 8 (#5156)
- add missing Perl extensions in easyconfig for Worker 1.6.7 (#5157)
- fix checksums for packages that download from ``github.com/x/y/archive`` (#5162)
- add missing libpng dependency to g2lib-1.4.0 easyconfig using intel-2017a (#5196)
- fix source_urls for Szip 2.1 & include SHA256 checksum (#5206)
- remove unneeded --with-fft-incs configure option for ABINIT (#5207)
- disable optarch for libjpeg-turbo 1.5.1 built with intel/2017a (#5214)
- update $R_LIBS in plotly easyconfig (#5215)
- include NLopt as a dependency in R easyconfigs that include nloptr as extension (#5217)
v3.4.0 (September 10th 2017)
----------------------------
feature release
- added easyconfigs for foss/2017b and intel/2017b common toolchains (#4768), (#4618)
- added new easyconfigs for existing toolchains:
- iomkl/2017b (#5097)
- added example easyconfig files for 31 new software packages:
- BAMM (#4650), BamM (#4650), bcl2fastq2 (#4902), CGNS (#5078), CLAPACK (#5096), CLISP (#4926, #4986),
cadaver (#4873), destiny (#5009), GroopM (#4650), Lucene-Geo-Gazetteer (#5064), libffcall (#4850),
libsigsegv (#4840), MERCKX (#5056), minimap2 (#4991), ncompress (#4852), OpenNLP (#5059, #5061),
OpenRefine (#5058), PHAST (#5096), PYTHIA (#5083), ParallelIO (#5071), PnetCDF (#5071), plotly (#5010),
QML (#5101), Quorum (#5095), Rcorrector (#5095), SCnorm (#5008), SOAPdenovo-Trans (#5095), Shannon (#5095),
Tika (#5063), UNAFold (#4997), VERSE (#4843)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1,
MRtrix 3.0_RC2, Perl 5.26.0, ROOT 6.10.04, Spark 2.2.0
- minor enhancements, including:
- add checksums to Perl 5.24.1 easyconfigs (#4973, #4992)
- add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (#5007, #5028, #5029, #5062, #5079)
- also define $INCLUDEPATH and $LIBRARY_PATH in Tesla-Deployment-Kit easyconfig (#5018)
- add check to see whether binutils is included as build dep when GCCcore toolchain is used (#5084)
- various bug fixes, including:
- added Rmpi patch file for R built with intel toolchains incl. impi 5.x (#4623)
- use single-line description in setup.py (#4881)
- fix version and source for Seurat + add extensions required by Seurat in R 3.4.0 easyconfig (#4889)
- add zlib as dependency to util-linux easyconfigs (#4900, #4998)
- use modextrapaths instead of modextravars in OpenMM easyconfig (#4903)
- update deprecated PLINK urls (#4920, #5006)
- fix moduleclass for Cookiecutter (#4947)
- fix order of OpenMPI dependency in iomkl easyconfig, must come after icc/ifort (#5024)
- fix typo in comment in util-linux easyconfigs & add SHA256 checksums (#5052)
- remove superfluous $CPATH update in GLib 2.44.0 easyconfig (#5053)
- update ncurses to not build a separate libtinfo but provide a soft link instead + force linking to ncurses in libreadline (#5067, #5074)
- include Autotools as build dep for netCDF (#5077)
- add missing binutils build dep for texinfo (#5099)
v3.3.1 (July 12th 2017)
-----------------------
bugfix/update release
- added example easyconfig files for 6 new software packages:
- FastME (#4811), geopy (#4821), Miniconda2 (#4841), ngmlr (#4818), OpenCoarrays (#4799), Seurat (#4832)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, numpy 1.13.0, Tensorflow 1.2.0
- minor enhancements, including:
- add SVG and Statistics::Basic to recent Perl versions (#4796)
- remove buildopts from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (#4779)
- include joblib as extension in recent Python easyconfigs (#4805)
- changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (#4807)
- get rid of references to 'hpcugent' organisation after move to github.com/easybuilders (#4815, #4837)
- add Rtsne as extension to R 3.4.0 (#4831)
- various bug fixes, including:
- use PYPI_SOURCE as source URL in Tensorflow easyconfigs (#4786)
- fix homepage for skewer (#4791)
- sync/fix source_urls & homepage in HDF5 easyconfig (#4800)
- fix ubsan error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 with system GCC 7.1 (#4813)
v3.3.0 (June 26th 2017)
-----------------------
feature release
- enable automatic style checks in easyconfig tests (#2506)
- added example easyconfig files for 28 new software packages:
- ada (#4594), Aspera-CLI (#4635), AUGUSTUS (#4624), ada (#4594), Bio-SamTools (#4637), Bpipe (#4590), BUSCO (#4624),
CNVnator (#4649), davix (#4755), EricScript (#4594), FUNWAVE-TVD (#4743), gmpy2 (#4609), gSOAP (#4755),
libsndfile (#4628), lpsolve (#4264), LUMPY (#4682), MaSuRCA (#4706), modred (#4729), MXNet (#4765),
NRGLjubljana (#4651), OrfM (#4703), Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603),
sharutils (#4745), Spyder (#4627), Tkinter (#4620), VariantMetaCaller (#4632)
- added new easyconfigs for existing toolchains:
- gimkl/2017a (#4646)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1
- minor enhancements, including:
- use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files (#4606, #4619)
- add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ libsndfile as dep) (#4628, #4680, #4747)
- also copy README for GapFiller (#4631)
- enable inclusion of version symbol by using --enable-ld-version-script configure option for LibTIFF (#4639)
- add SHA256 checksums for libpciaccess to discriminate from old tarballs that required running autogen.sh (#4688)
- fix NE_GLOBAL_DIR path for ne by also specifying PREFIX in buildopts (#4698)
- more (trivial) style fixes (#4761)
- avoid use of import in ANSYS & MATLAB easyconfigs (#4762)
- set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763)
- avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764)
- add the docopt module to all Python 2017a easyconfigs (#4770)
- stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (#4774)
- various bug fixes, including:
- fix typo in statsmodels source url (/sources/ -> /source/) (#4612)
- add location to DotLib.pm to $PERL5LIB for SSPACE_Basic (#4638)
- add missing /gnu/ ins ftpmirror.gnu.org source_urls, or use GNU_SOURCE where possible (#4653)
- consistently use --with-harfbuzz=no configure option in freetype easyconfigs (#4668)
- use --with-x=yes in R easyconfigs that include X11 as a dependency (#4701)
- remove '4.0' in tbb description (#4707)
- add lib sanity check paths for Debian compatibility in nettle (#4722)
- fix source URLs for HDF5 (#4749)
v3.2.1 (May 12th 2017)
----------------------
bugfix/update release
- added example easyconfig files for 12 new software packages:
- AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544),
NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556)
- added new easyconfigs for existing toolchains:
- goolfc 2017.01 (#4577)
- added additional easyconfigs for various supported software packages, including:
- HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0
- minor enhancements, including:
- update source URLs in libpciaccess easyconfigs (#3960)
- enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555)
v3.2.0 (May 5th 2017)
---------------------
feature release
- added example easyconfig files for 34 new software packages:
- ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484),
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)