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869 Commits

Author SHA1 Message Date
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
Sergei Trofimovich
eb0590ec3d kssd: pull upstream fix for -fno-common tollchains 
Without the change build fails on upstream gcc-10 as:

    ld: ccD2iWhk.o:(.bss+0x8): multiple definition of `domain';
      ccgA4lYl.o:(.bss+0x8): first defined here
    ld: ccD2iWhk.o:(.bss+0x0): multiple definition of `long_domain';
      ccgA4lYl.o:(.bss+0x0): first defined here
 2022-05-21 11:22:53 +01:00
Ben Darwin
5cf446f41b ezminc: mark broken 
Package refuses to build with current GCC (11), but building with older
GCC causes error linking libminc and I don't want to pin a bunch of
deps.

A newer version is available upstream but it only works with ITK 5.0
(see https://github.com/BIC-MNI/EZminc/issues/15),
but we have 4.x and 5.2.x in tree and I'm reluctant to add 5.0 just for
one package (even ITK 4.x is only used by ants and ezminc and should be
removed as soon as ants is upgraded).
 2022-05-17 10:24:07 -07:00
Sergei Trofimovich
deaab56289 freebayes: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: foomatic_rip-options.o:/build/foomatic-filters-4.0.17/options.c:49: multiple definition of `cupsfilter';
      foomatic_rip-foomaticrip.o:/build/foomatic-filters-4.0.17/foomaticrip.c:158: first defined here
 2022-05-14 13:19:17 +01:00
Thomas Gerbet
44c1590f1f bayescan: fix the build 
Moved back to C++14 to avoid the new errors and warnings introduced with
C++17.
 2022-05-13 12:00:08 +02:00
Theodore Ni
81046b393b
bowtie: fix build on case insensitive file systems 
Add a patch that removes the current source directory from the include
search path during compilation so that #include <version> does not end
up picking the VERSION source code file.
 2022-05-11 03:20:03 -05:00
Theodore Ni
802a8416b6
bowtie: add arm64 patch to build on M1 Macs 
This does not fix the build on Macs, but it brings the build on M1 Macs
to parity with non-M1 Macs.
 2022-05-11 02:36:56 -05:00
Sergei Trofimovich
428045f39b bwa: pull upstream fix for -fno-common tollchains 
Without the change build fails on -fno-common toolchains like upstream
gcc-10 as:

    $ nix build -L --impure --expr 'with import ./. {}; bwa.overrideAttrs (oa: {   NIX_CFLAGS_COMPILE = (oa.NIX_CFLAGS_COMPILE or "") + "-fno-common"; })'
    ...
    ld: ./libbwa.a(rope.o):/build/bwa-0.7.17/rle.h:33:
      multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
    ld: ./libbwa.a(rle.o):/build/bwa-0.7.17/rle.h:33:
      multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
 2022-05-08 08:56:43 +01:00
Luis Pedro Coelho
596c5e7ea2 Static bwa 
AR needs to be passed specifically on the command line
 2022-05-04 02:20:50 +02:00
Luis Pedro Coelho
4758873378 Static build for samtools 
Curses is not supported (it may be possible to support it)
 2022-05-04 02:16:17 +02:00
Luis Pedro Coelho
0b1c28d5a1 Static build for megahit 2022-05-04 02:13:31 +02:00
Vladimír Čunát
c480cc2895
Merge branch 'master' into staging-next-2022-04-23 2022-04-30 23:02:28 +02:00
R. Ryantm
a82b1b63c3 blast: 2.12.0 -> 2.13.0 2022-04-29 09:39:10 -05:00
github-actions[bot]
073cad8fd6
Merge master into staging-next 2022-04-25 12:04:02 +00:00
Sandro
2f517412c4
Merge pull request #165477 from rbreslow/dcm2niix-optional-modules 2022-04-25 11:59:49 +02:00
Rocky Breslow
d1c3fea7ec
dcm2niix: support usage of suggested Cloudflare zlib 2022-04-18 15:00:45 -04:00
Rocky Breslow
9019ce0106
dcm2niix: add maintainer 
Also, fix grammatical error in long description.
 2022-04-18 15:00:16 -04:00
Ben Siraphob
259fa13d53 treewide: remove nativeBuildInputs that are in stdenv 2022-04-16 21:46:46 +03:00
Fabián Heredia Montiel
8a9d5e296b cmtk: add -std=c++11 to fix build on gcc11 2022-04-15 11:15:30 -05:00
Malo Bourgon
0e802eafad treewide: add meta.mainProgram to many packages 2022-04-14 10:24:01 -07:00
Artturi
ebf6f84ea2
Merge pull request #164722 from armeenm/bump-eggnog-mapper 
eggnog-mapper: 1.0.3 -> 2.1.7
 2022-04-10 14:37:21 +03:00
Rocky Breslow
09b7444b82
dcm2niix: add support for configuring optional compile-time modules 
Right now, the dcm2niix package produces a single binary without support for
dcm2niibatch, JPEG-LS, OpenJPEG, or an alternative zlib library. The official
build process for dcm2niix configures all these options (minus batch support). I
was motivated to make these changes so my organization could process JPEG 2000
imagery using the Nix binary.
 2022-04-04 10:41:27 -04:00
ajs124
60f1e6ffe2 ncbi_tools: remove after being marked broken for over two years 
It was marked in commit b9948fedc6 by Robin Gloster on 2017-03-30 (commited on 2017-03-30)
 2022-04-03 16:14:18 +01:00