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1157 Commits

Author SHA1 Message Date
OTABI Tomoya
0a18e1f929
Merge pull request #249750 from natsukium/bioawk/init 
bioawk: init at unstable-2017-09-11
 2023-10-20 17:59:30 +09:00
natsukium
056f9e21c0
bowtie2: enable tests 2023-10-20 17:08:20 +09:00
natsukium
13fe1effaf
bowtie2: fix build on aarch64 2023-10-20 17:07:55 +09:00
natsukium
aae51697be
bowtie2: refactor 2023-10-20 17:06:09 +09:00
scalavision
9fd3ea0f76 deeptools: 3.5.1 -> 3.5.4 2023-10-18 19:06:01 +02:00
R. Ryantm
355e594816 raxml: 8.2.12 -> 8.2.13 2023-10-16 22:16:12 +00:00
R. Ryantm
d89c2af58a bowtie2: 2.5.1 -> 2.5.2 2023-10-14 10:06:32 +00:00
OTABI Tomoya
e8f331680d
Merge pull request #259418 from natsukium/blast-bin/update 
blast-bin: 2.13.0 -> 2.14.1
 2023-10-12 23:49:59 +09:00
natsukium
d60c85fb75
blast-bin: add sourceProvenance to meta 2023-10-07 10:12:24 +09:00
natsukium
3dc0f1e7b7
blast-bin: 2.13.0 -> 2.14.1 
Changelog: https://www.ncbi.nlm.nih.gov/books/NBK131777/#_Blast_ReleaseNotes_BLAST_2_14_1_August_2_
 2023-10-07 01:59:18 +09:00
natsukium
96178c29a4
truvari: 4.0.0 -> 4.1.0 
Diff: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0

Changelog: https://github.com/ACEnglish/truvari/releases/tag/v4.1.0
 2023-10-07 01:30:27 +09:00
natsukium
776b2694a3
truvari: add meta.changelog 2023-10-07 01:30:27 +09:00
Justin Bedo
e347cca9f8
delly: 1.1.6 -> 1.1.7 
Diff: https://github.com/dellytools/delly/compare/v1.1.6...1.1.7
 2023-10-06 14:12:05 +11:00
Weijia Wang
0396d3b0fb
Merge pull request #258254 from r-ryantm/auto-update/nest-mpi 
nest-mpi: 3.5 -> 3.6
 2023-10-01 03:53:05 +02:00
Weijia Wang
d2f79d7443
Merge pull request #257369 from r-ryantm/auto-update/stacks 
stacks: 2.62 -> 2.65
 2023-10-01 03:20:19 +02:00
Weijia Wang
293062bbdb stacks: set platforms 2023-10-01 02:26:34 +02:00
Weijia Wang
00d57438ab
Merge pull request #256805 from r-ryantm/auto-update/neuron-mpi 
neuron-mpi: 8.2.2 -> 8.2.3
 2023-10-01 00:44:58 +02:00
R. Ryantm
a78f4ed541 nest-mpi: 3.5 -> 3.6 2023-09-30 18:54:13 +00:00
natsukium
c90607c5a7
dssp: 4.4.2 -> 4.4.3 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.2...v4.4.3

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.3
 2023-09-28 15:38:55 +09:00
R. Ryantm
90361534b7 stacks: 2.62 -> 2.65 2023-09-26 03:03:04 +00:00
github-actions[bot]
3e52e5929d
Merge master into staging-next 2023-09-25 12:01:02 +00:00
Mario Rodas
b289d79b8d hmmer: add changelog to meta 2023-09-24 04:24:00 +00:00
R. Ryantm
272a0e1edb hmmer: 3.3.2 -> 3.4 2023-09-24 04:23:47 +00:00
R. Ryantm
d660b340ee neuron-mpi: 8.2.2 -> 8.2.3 2023-09-23 02:33:53 +00:00
github-actions[bot]
583877beb2
Merge master into staging-next 2023-09-22 18:01:00 +00:00
László Kupcsik
c678bba28c trimmomatic: init at 0.39 
Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>
 2023-09-22 13:50:18 -03:00
github-actions[bot]
3245a21e71
Merge master into staging-next 2023-09-19 06:01:00 +00:00
R. Ryantm
65033fea28 mosdepth: 0.3.4 -> 0.3.5 2023-09-19 00:55:31 +00:00
github-actions[bot]
9fd6a65a3a
Merge master into staging-next 2023-09-18 12:01:07 +00:00
R. Ryantm
e567f85a64 blast: 2.14.0 -> 2.14.1 2023-09-16 03:10:11 +00:00
Alyssa Ross
4a027948f9
Merge remote-tracking branch 'origin/staging-next' into staging 
Conflicts:
	pkgs/applications/radio/soapysdr/default.nix
 2023-09-14 11:31:01 +00:00
Mario Rodas
48780fa239
Merge pull request #250309 from trofi/angsd-fix-parallel 
angsd: pull patch pending upstream inclusion for parallel build fix
 2023-09-13 06:24:00 -05:00
github-actions[bot]
564dc31f47
Merge staging-next into staging 2023-09-12 18:01:30 +00:00
R. Ryantm
d5e6e8ac03 veryfasttree: 4.0.2 -> 4.0.3 2023-09-12 06:13:28 +00:00
github-actions[bot]
6d1f33a3ed
Merge staging-next into staging 2023-09-09 12:01:22 +00:00
R. Ryantm
ac77a8f7d0 igv: 2.16.1 -> 2.16.2 2023-09-09 05:56:58 +00:00
Sandro Jäckel
fccf04b620 treewide: replace -DCMAKE_BUILD_TYPE in cmakeFlags with cmakeBuildType 2023-09-08 14:18:26 +00:00
Ben Darwin
5bbcb4840b mrtrix: unstable-2021-11-25 -> 3.0.4 2023-09-06 12:11:38 -04:00
Pol Dellaiera
55b00aa1f7
ants: update postInstall attribute 2023-09-02 23:09:28 +02:00
Pol Dellaiera
ad1e8a5b43
ants: update meta attributes 2023-09-02 23:08:44 +02:00
Pol Dellaiera
d04a1a598e
ants: use finalAttrs pattern 2023-09-02 22:18:19 +02:00
Pol Dellaiera
35145f9df0
ants: reformat file using nixpkgs-fmt 2023-09-02 22:17:19 +02:00
R. Ryantm
875e737bfa ants: 2.4.4 -> 2.5.0 2023-09-02 11:57:30 +00:00
Justin Bedő
f25f30b17a
Merge pull request #251304 from r-ryantm/auto-update/sambamba 
sambamba: 1.0.0 -> 1.0.1
 2023-09-01 15:30:29 +10:00
github-actions[bot]
e79f8fd118
Merge master into staging-next 2023-08-25 18:00:58 +00:00
R. Ryantm
e1b695a96f iqtree: 2.2.2.6 -> 2.2.2.7 2023-08-25 12:25:13 +00:00
R. Ryantm
d564dfa4d0 sambamba: 1.0.0 -> 1.0.1 2023-08-25 06:20:00 +00:00
github-actions[bot]
a451dcf514
Merge master into staging-next 2023-08-24 06:01:14 +00:00
OTABI Tomoya
21943b1829
Merge pull request #248172 from alxsimon/bwa 
bwa-mem2: init at version 2.2.1
 2023-08-24 09:28:34 +09:00
Alexis Simon
556dac0725 bwa-mem2: init at version 2.2.1 
Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>
 2023-08-23 15:02:06 -07:00
github-actions[bot]
56f5b9fafc
Merge staging-next into staging 2023-08-21 12:01:35 +00:00
OTABI Tomoya
325b09c1b5
Merge pull request #249878 from jbedo/last 
last: 1460 -> 1471
 2023-08-21 16:09:10 +09:00
Emery Hemingway
ed353dc721 mosdepth: build with Nim-2 2023-08-21 07:32:46 +01:00
Emery Hemingway
9025a583b1 nimPackages.hts: 0.3.4 -> 0.3.23, rename from hts-nim 2023-08-21 07:32:46 +01:00
Sergei Trofimovich
f434e83d62 angsd: pull patch pending upstream inclusion for parallel build fix 
Without the change rapallel builds fail occasionally as:

    $ make --shuffle -j
    ...
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   argStruct.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   ancestral_likes.cpp
    gcc -c   -O3 -D__STDC_FORMAT_MACROS   fet.c
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   abcGL.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   pop1_read.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   angsd.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   abcHWE_F.cpp
    gcc -c   -O3 -D__STDC_FORMAT_MACROS   kprobaln.c
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   mpileup.cpp
    argStruct.cpp:3:10: fatal error: version.h: No such file or directory
        3 | #include "version.h"
          |          ^~~~~~~~~~~
    compilation terminated.
    angsd.cpp:11:10: fatal error: version.h: No such file or directory
       11 | #include "version.h"
          |          ^~~~~~~~~~~
 2023-08-20 08:50:53 +01:00
github-actions[bot]
9145b3fd81
Merge staging-next into staging 2023-08-19 18:01:22 +00:00
Justin Bedo
8d9f56ac2d
last: 1460 -> 1471 
Diff: https://gitlab.com/mcfrith/last/-/compare/refs/tags/1460...1471
 2023-08-18 14:11:53 +10:00
natsukium
86f362ce5b
bioawk: init at unstable-2017-09-11 2023-08-18 00:36:09 +09:00
natsukium
5462f67cc8
bamtools: init at 2.5.2 2023-08-18 00:17:15 +09:00
Pol Dellaiera
3eb7f7a63b
Merge pull request #248683 from oxij/tree/source-root-continues-3 
treewide: cleanup `sourceRoot` and `setSourceRoot` usage
 2023-08-15 05:53:52 +02:00
Jan Malakhovski
d098c821d6 treewide: remove unneeded dots and slashes in sourceRoots 2023-08-12 08:29:56 +00:00
Theodore Ni
851d2f6b95
macs2: 2.2.8 -> 2.2.9.1 2023-08-11 14:45:45 -07:00
R. Ryantm
6d530a6389 seqkit: 2.5.0 -> 2.5.1 2023-08-10 04:42:38 +00:00
R. Ryantm
a303664816 samtools: 1.17 -> 1.18 2023-08-07 01:22:06 +00:00
Mario Rodas
156a49aa49
Merge pull request #236810 from natsukium/cmtk/update 
cmtk: 3.3.1 -> 3.3.2; fix darwin build
 2023-08-06 11:51:18 -05:00
Weijia Wang
5c9ba9e55c
Merge pull request #246863 from r-ryantm/auto-update/picard-tools 
picard-tools: 3.0.0 -> 3.1.0
 2023-08-04 21:17:27 +02:00
Jan Malakhovski
5852f26bdc treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases 2023-08-03 16:32:03 +00:00
R. Ryantm
29a0a9e29a picard-tools: 3.0.0 -> 3.1.0 2023-08-02 22:03:03 +00:00
Weijia Wang
66aedfd010
Merge pull request #246815 from r-ryantm/auto-update/veryfasttree 
veryfasttree: 4.0.1 -> 4.0.2
 2023-08-02 21:56:37 +02:00
Weijia Wang
e4e313aeff
Merge pull request #246485 from r-ryantm/auto-update/bcftools 
bcftools: 1.17 -> 1.18
 2023-08-02 19:51:47 +02:00
Pol Dellaiera
9a772d7658
veryfasttree: use finalAttrs pattern 2023-08-02 18:51:11 +02:00
R. Ryantm
1fd16883d4 veryfasttree: 4.0.1 -> 4.0.2 2023-08-02 16:13:45 +00:00
Weijia Wang
23332e13fe
Merge pull request #243407 from natsukium/paml/update 
paml: 4.9j -> 4.10.7
 2023-08-01 22:09:44 +02:00
R. Ryantm
487c6ac2bd bcftools: 1.17 -> 1.18 2023-08-01 03:38:31 +00:00
R. Ryantm
40b736f0e8 last: 1456 -> 1460 2023-07-25 04:34:13 +00:00
github-actions[bot]
449a683b10
Merge master into staging-next 2023-07-24 00:02:26 +00:00
natsukium
e54f06de69
dssp: 4.3.1 -> 4.4.2 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.3.1...v4.4.2

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.2
 2023-07-23 21:24:23 +09:00
Tobias Mayer
ba2ce6e73b
various packages: pin boost179 
Taken from PR #244831 and vcunat amended the miopen override.
 2023-07-22 16:54:22 +02:00
R. Ryantm
7a9d01d44c seqkit: 2.4.0 -> 2.5.0 2023-07-17 11:15:14 +00:00
natsukium
d2c506948b
paml: refactor 2023-07-14 15:08:14 +09:00
natsukium
f6e2b68122
paml: 4.9j -> 4.10.7 
Diff: d59d538939...4.10.7
Changelog: https://github.com/abacus-gene/paml/releases/tag/4.10.7
 2023-07-14 15:08:08 +09:00
natsukium
7cec88e50f
delly: enable openmp 2023-07-14 00:20:20 +09:00
natsukium
ae95c0d5a5
delly: refactor 2023-07-14 00:18:27 +09:00
natsukium
61be2ca18a
delly: enable darwin support 
- add passthru.tests
 2023-07-13 23:54:39 +09:00
natsukium
e7c8cbc2b1
cmtk: fix format 
- use finalAttrs instead of rec
- fix license
- remove trailing space from description
 2023-07-11 17:50:47 +09:00
natsukium
7014b723d9
cmtk: enable some compile options 
- use system zlib
- enabled bzip2
- enabled fftw
- enabled openmp for clang

- still disabled Grand Central Dispatch for linux because of build failure
- still disabled CUDA because of build failure
- still disabled mxml because of build failure
- still disabled lzma because of lack of lzmadec.h
- still disabled dcmtk because of build failure
 2023-07-11 17:50:47 +09:00
natsukium
6bf04fc9c9
cmtk: fix darwin build 2023-07-11 17:50:43 +09:00
R. Ryantm
b5e04f0bc7 kallisto: 0.48.0 -> 0.50.0 2023-07-09 17:19:43 +00:00
Weijia Wang
6d506a9d51
Merge pull request #242302 from r-ryantm/auto-update/nest-mpi 
nest-mpi: 3.4 -> 3.5
 2023-07-09 12:21:22 +03:00
R. Ryantm
ead7b7800d nest-mpi: 3.4 -> 3.5 2023-07-08 16:03:30 +00:00
R. Ryantm
47d5bee543 veryfasttree: 4.0 -> 4.0.1 2023-07-08 07:27:05 +00:00
Weijia Wang
1e0d363214
Merge pull request #241136 from r-ryantm/auto-update/veryfasttree 
veryfasttree: 3.1.1 -> 4.0
 2023-07-03 17:17:51 +03:00
Weijia Wang
82d4f6b43d veryfasttree: fix build on darwin 2023-07-03 12:29:44 +03:00
Martin Weinelt
bb40b8c205
Merge pull request #235322 from natsukium/dssp/update 
dssp: 4.2.2.1 -> 4.3.1; libcifpp: 5.0.8 -> 5.1.0.1; libmcfp: 1.2.3 -> 1.2.4
 2023-07-02 23:12:49 +02:00
figsoda
50acc2d57a pkgs/applications: replace "${version}" with version 2023-07-02 14:39:50 -04:00
R. Ryantm
cb16c50571 veryfasttree: 3.1.1 -> 4.0 2023-07-02 15:55:36 +00:00
natsukium
7b49fced0f
dssp: fix format 
- add changelog to meta
- use finalAttrs
 2023-07-01 16:40:29 +09:00
natsukium
fba5a4d702
dssp: 4.2.2.1 -> 4.3.1 
Diff: https://github.com/PDB-REDO/dssp/compare/v4.2.2.1...v4.3.1
 2023-07-01 16:36:36 +09:00
R. Ryantm
abfcd95c63 mosdepth: 0.3.3 -> 0.3.4 2023-06-28 10:52:42 +00:00
Weijia Wang
826bdb7214
Merge pull request #239691 from r-ryantm/auto-update/diamond 
diamond: 2.1.7 -> 2.1.8
 2023-06-26 07:46:03 +02:00