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891 commits

Author SHA1 Message Date
thyol cdcb7946ba veryfasttree: init at 3.1.1 2022-11-22 20:45:45 +01:00
thyol 35d3a6fa79 muscle: add myself to maintainers 2022-11-22 20:19:17 +01:00
thyol d7c8595f62 muscle: 3.8.31 -> 5.1.0 2022-11-22 20:19:17 +01:00
thyol 81d6f1c7dc sratoolkit: init at 2.11.3 2022-11-21 20:27:28 +01:00
R. Ryantm 6ba0d20487 igv: 2.14.1 -> 2.15.1 2022-11-20 14:06:29 +08:00
Jiajie Chen fc2812a1f8 nest: init at 3.3 2022-11-10 09:20:41 +08:00
R. Ryantm c7ba9b459c delly: 1.1.5 -> 1.1.6 2022-11-08 18:21:37 +00:00
Justin Bedő 3a90ab68e6
Merge pull request #197631 from jbedo/octopus 
octopus-caller: backport patch to fix build
 2022-11-07 21:26:21 +00:00
Bruno Bzeznik 9243a44c9c seqkit: init at 2.3.1 2022-11-04 08:51:32 +01:00
Stanisław Pitucha 9ed8ce7ff3
Merge pull request #198609 from natsukium/mmseqs2/init 
mmseqs2: init at 14-7e284
 2022-11-01 21:47:20 +11:00
natsukium ed7511ad02
mmseqs2: init at 14-7e284 2022-10-31 23:49:10 +09:00
Justin Bedo 5f5bb45093
octopus-caller: backport patch to fix build 2022-10-25 09:52:28 +11:00
OPNA2608 982a1bfd80 sambamba: fix compilation on Darwin, cleanup installPhase 2022-10-23 16:12:47 +02:00
Jan Tojnar 457f28f6f8 Merge branch 'master' into staging-next 
; Conflicts:
;	pkgs/development/tools/codespell/default.nix

codespell 2.2.2 switched to pyproject & setuptools_scm:
https://github.com/codespell-project/codespell/pull/2523
 2022-10-19 05:24:28 +02:00
R. Ryantm 4ab06e3223 ants: 2.4.1 -> 2.4.2 2022-10-19 09:19:31 +08:00
github-actions[bot] f52955a521
Merge master into staging-next 2022-10-16 18:01:42 +00:00
R. Ryantm 00b3b4ee24 gatk: 4.2.6.1 -> 4.3.0.0 2022-10-16 21:48:30 +08:00
Martin Weinelt 51fcbf5bb7 Merge remote-tracking branch 'origin/master' into staging-next 2022-10-16 00:18:40 +02:00
Jonas Heinrich 9259c4b841
Merge pull request #195990 from r-ryantm/auto-update/angsd 
angsd: 0.938 -> 0.940
 2022-10-15 09:33:23 +02:00
github-actions[bot] 886633ba43
Merge master into staging-next 2022-10-15 00:04:00 +00:00
R. Ryantm 4cee9b9ddb angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
Artturi e66d2fd89d
Merge pull request #194256 from Artturin/treewides2 2022-10-13 00:08:01 +03:00
Markus S. Wamser c9d167f174 pkgs.applications: remove unused args 2022-10-12 16:00:16 +02:00
Martin Weinelt cf7f4393f3
Merge pull request #193494 from NixOS/staging-next 2022-10-11 01:12:59 +02:00
Alexis Praga 2ce78bd571 gatk: add java and python to PATH 
gatk is actually a python script that starts either the local or spark
.jar file according to a fixed setup.
In the initial commit, neither java nor python were present in PATH.
 2022-10-10 23:06:01 +02:00
Artturin 7e49471316 treewide: optional -> optionals where the argument is a list 
the argument to optional should not be list
 2022-10-10 15:40:21 +03:00
R. Ryantm 92bc5dbbae picard-tools: 2.27.4 -> 2.27.5 2022-10-08 00:09:59 +00:00
github-actions[bot] f18d801779
Merge staging-next into staging 2022-09-28 18:05:53 +00:00
R. Ryantm ddf9f1800a delly: 1.1.3 -> 1.1.5 2022-09-27 11:26:09 +00:00
Artturin 0734f54ef2 treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs 
found with nixpkgs-lint
 2022-09-26 17:53:26 +03:00
Justin Bedő d21b5ac044
Merge pull request #192211 from r-ryantm/auto-update/last 
last: 1409 -> 1411
 2022-09-26 11:49:30 +10:00
Brad Langhorst 2beb26b45b seqtk: init at 1.3 
Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>
 2022-09-25 19:55:58 -04:00
R. Ryantm 1008651931 last: 1409 -> 1411 2022-09-21 08:24:01 +00:00
Christian Kögler e06e88d003
Merge pull request #189923 from r-ryantm/auto-update/igv 
igv: 2.14.0 -> 2.14.1
 2022-09-18 15:59:16 +02:00
R. Ryantm 9da745bfaf messer-slim: 4.0 -> 4.0.1 2022-09-15 22:25:51 +00:00
Sandro 785031e430
Merge pull request #185819 from apraga/gatk-4.2.6.1 2022-09-10 21:31:42 +02:00
natsukium 9e65d09e3d
mafft: 7.505 -> 7.508 
changed to fetch from new gitlab repository
 2022-09-09 13:26:38 +09:00
R. Ryantm c7832514ef igv: 2.14.0 -> 2.14.1 2022-09-05 22:29:15 +00:00
Sandro ef987a9604
Merge pull request #189329 from bcdarwin/itk4-removal 2022-09-05 16:05:51 +02:00
Sandro 73bf7a0ca0
Merge pull request #181954 from bzizou/treemix 2022-09-05 15:57:48 +02:00
Bruno Bzeznik 7c09cfdc1a treemix: init at 1.13 2022-09-05 06:55:03 +02:00
Jonas Heinrich eb3d3b2e90
Merge pull request #175449 from bzizou/iqtree 
iqtree: init at 2.2.0.4
 2022-09-04 23:58:04 +02:00
Ben Darwin 1280129aab EZminc: itk4 -> itk (formally; package is broken) 2022-09-04 13:36:24 -04:00
Ben Darwin 961b308fe1 ants: 2.2.0 -> 2.4.1 2022-09-04 13:36:24 -04:00
Alexis Praga 95da303902 gatk : init at 4.2.6.1 
GATK is the industry standard for genetics analysis, more precisely for
identifying SNPs and indels in germline DNA and RNAseq data .
This package does not ship the Spark version.

Apply suggestions from code review
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-09-04 15:34:30 +02:00
Jonas Heinrich 3b3a01e3f9
Merge pull request #188785 from jbedo/last 
last: 1406 -> 1409
 2022-09-04 12:40:30 +02:00
Justin Bedo d9acf90371
last: 1406 -> 1409 2022-09-04 10:36:01 +10:00
Sandro 9b214e6dad
Merge pull request #177830 from r-ryantm/auto-update/eggnog-mapper 2022-09-03 22:43:11 +02:00
Jonas Heinrich ed227dc9fb
Merge pull request #168109 from r-ryantm/auto-update/bcftools 
bcftools: 1.15 -> 1.16
 2022-08-27 08:51:34 +02:00
Jonas Heinrich 21ba29f226
Merge pull request #181338 from thyol/diamond 
diamond: 0.8.36 -> 2.0.15
 2022-08-25 15:25:03 +02:00
Jonas Heinrich b8e0c9b652
Merge pull request #183253 from r-ryantm/auto-update/angsd 
angsd: 0.937 -> 0.938
 2022-08-24 10:35:05 +02:00
Jonas Heinrich c199cfabff
Merge pull request #184694 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.15.4 -> 3.15.5
 2022-08-23 20:21:42 +02:00
Jonas Heinrich 5cb64f6046
Merge pull request #186958 from r-ryantm/auto-update/igv 
igv: 2.13.2 -> 2.14.0
 2022-08-21 21:11:49 +02:00
R. Ryantm 49f4071f30 eggnog-mapper: 2.1.7 -> 2.1.9 2022-08-21 12:45:21 +00:00
Jonas Heinrich 8508d5decf
Merge pull request #183724 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.26.11 -> 2.27.4
 2022-08-21 10:03:42 +02:00
R. Ryantm 98d1f4c35d bcftools: 1.15 -> 1.16 2022-08-18 18:44:42 +00:00
R. Ryantm f4c3ff2d7f igv: 2.13.2 -> 2.14.0 2022-08-16 13:24:02 +00:00
R. Ryantm c37112d2d0 messer-slim: 3.7.1 -> 4.0 2022-08-14 14:11:37 +00:00
Mario Rodas 0cab4c8f8a
Merge pull request #183012 from bcdarwin/update-mni-autoreg 
mni_autoreg: unstable-2017-09-22 -> unstable-2022-05-20
 2022-08-13 01:05:26 -05:00
Mario Rodas 6aeb44c32e
Merge pull request #185211 from r-ryantm/auto-update/delly 
delly: 1.0.3 -> 1.1.3
 2022-08-13 00:41:48 -05:00
kilianar 0442ab82e0 igv: 2.8.13 -> 2.13.2 
- https://software.broadinstitute.org/software/igv/2.9.x
- https://software.broadinstitute.org/software/igv/2.10.x
- https://software.broadinstitute.org/software/igv/2.11.x
- https://software.broadinstitute.org/software/igv/2.12.x
- https://software.broadinstitute.org/software/igv/2.13.x
 2022-08-07 17:53:06 +02:00
Bobby Rong 934c6c9a95
Merge pull request #184334 from r-ryantm/auto-update/mafft 
mafft: 7.490 -> 7.505
 2022-08-07 16:18:05 +08:00
R. Ryantm 8b7c09d0e6 delly: 1.0.3 -> 1.1.3 2022-08-05 08:58:15 +00:00
Sandro e9984bc607
Merge pull request #182705 from luispedro/no_test_samtools_on_cross_compile 2022-08-02 23:20:38 +02:00
Luis Pedro Coelho 5877d8e072 samtools: Fix cross-compilation 
Tests require bgzip which comes from the htslib package.

This did not cause problems prior to
41485e7337 as tests were not run in
cross-compilation.
 2022-08-02 17:52:50 +02:00
Sandro e76aa82431
Merge pull request #184598 from wegank/treewide-fix-platforms 2022-08-02 15:57:56 +02:00
R. Ryantm 921b81745d SPAdes: 3.15.4 -> 3.15.5 2022-08-02 02:26:56 +00:00
Weijia Wang 278086eddb treewide: fix platforms 2022-08-01 18:33:27 +02:00
R. Ryantm b2bbba02ba mafft: 7.490 -> 7.505 2022-07-31 20:32:57 +00:00
R. Ryantm e0a9011556 last: 1268 -> 1406 2022-07-31 16:58:20 +00:00
R. Ryantm 9338d8c9b7 picard-tools: 2.26.11 -> 2.27.4 2022-07-29 16:12:10 +00:00
R. Ryantm 8c0e56fc14 angsd: 0.937 -> 0.938 2022-07-28 07:50:11 +00:00
Justin Bedő 9e80da74b0
Merge pull request #182028 from jbedo/bedops 
bedops: 2.4.40 -> 2.4.41
 2022-07-28 09:14:23 +10:00
Ben Darwin 125da19866 mni_autoreg: unstable-2017-02-22 -> unstable-2022-05-20 2022-07-26 16:03:12 -04:00
natsukium cf0dc604a6
dssp: init at 4.0.5 2022-07-19 12:17:34 +09:00
Justin Bedo 99fb9abfaa
bedops: 2.4.40 -> 2.4.41 2022-07-19 09:09:52 +10:00
Lassulus 01853c3bcc
Merge pull request #174547 from r-ryantm/auto-update/delly 
delly: 0.9.1 -> 1.0.3
 2022-07-16 10:49:50 +02:00
Pascal Wittmann 26ddf3454a
Merge pull request #138255 from natsukium/mafft/init 
mafft: init at 7.487
 2022-07-16 00:54:59 +02:00
thyol 0d6e3afdba diamond: update metadata 2022-07-13 12:33:33 +02:00
thyol 55853ae096 maintainers: add thyol 2022-07-13 12:30:44 +02:00
thyol 4e79b5e370 diamond: remove patch 2022-07-13 11:58:39 +02:00
thyol 5e765ecc68 diamond: 0.8.36 -> 2.0.15 2022-07-13 11:58:02 +02:00
R. Ryantm 5ea1c721e1 delly: 0.9.1 -> 1.0.3 2022-07-07 22:10:48 +00:00
ajs124 3b5f125515 maintainers: remove metabar 
no github account + only commit is 78c052e91a
 2022-06-29 00:52:13 +02:00
Robert Scott 466c2e342a treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
Robert Scott 444d3a825a treewide/python-modules: add sourceProvenance for several packages 2022-06-20 09:43:10 +02:00
Sandro Jäckel 0f14467d44
MACS2: mark broken 2022-06-06 11:46:22 -07:00
Robert Scott 3b6bc4b69c treewide: set sourceProvenance for packages containing downloaded jars 
these are the easily identifiable cases and will not be comprehensive
 2022-06-04 19:47:57 +01:00
Sergei Trofimovich fd48676596
Merge pull request #175259 from trofi/workaround-fno-common-for-svaba 
svaba: add -fcommon workaround
 2022-06-03 05:59:16 +00:00
ckie 958fcfb4fa
Merge pull request #175477 from bzizou/astral 
astral: init at 5.7.1
 2022-05-31 14:55:37 +03:00
Bruno Bzeznik 376897ced3 astral: init at 5.7.1 2022-05-31 09:03:24 +02:00
Rick van Schijndel 433701147a
treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
Bruno Bzeznik c15d568d0b iqtree: init at 2.2.0.4 2022-05-30 10:53:40 +02:00
Rick van Schijndel 37c633f7ae treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
Sergei Trofimovich 2f60be03bb svaba: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of
      `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here
 2022-05-29 08:07:23 +01:00
Rick van Schijndel 331e26b6ec
Merge pull request #173867 from trofi/fix-fno-common-for-kssd 
kssd: pull upstream fix for -fno-common tollchains
 2022-05-28 20:39:38 +02:00
Sandro 3b9985498d
Merge pull request #174036 from trofi/workaround-fno-common-for-paml 
paml: add -fcommon workaround
 2022-05-25 00:35:00 +02:00
Sergei Trofimovich 8cba3775d8 paml: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes';
      /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here
 2022-05-22 20:23:12 +01:00
Sergei Trofimovich 94a5ae4f91 mni_autoreg: pull upstream workaround for -fno-common toolchains 
Without the change build fails on upstream gcc-10 as:

    ld: lib_minctracc.a(minctracclib.c.o):(.bss+0x78): multiple definition of
      `prog_name'; CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o:(.bss+0x18): first defined here
 2022-05-22 14:37:30 +01:00
Bobby Rong 3b468e68b7
Merge pull request #173017 from trofi/workaround-fno-common-for-freebayes 
freebayes: add -fcommon workaround
 2022-05-22 13:39:14 +08:00