Justin Bedo
8c5251e3c0
bowtie2: fix missing dependencies
2018-12-05 10:51:30 +11:00
R. RyanTM
36a0335d02
picard-tools: 2.18.14 -> 2.18.17 ( #50647 )
...
* picard-tools: 2.18.14 -> 2.18.16
Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.16
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
* picard-tools: 2.18.16 -> 2.18.17
Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.17
2018-11-27 14:31:09 +01:00
Ben Darwin
cb6d819b93
niftyseg: init at 1.0.0
2018-11-16 12:29:29 -05:00
Ben Darwin
6aa3deeb50
niftyreg: init at 1.3.9
2018-11-16 12:24:53 -05:00
Markus J. Ankenbrand
bf05da0967
hmmer: 3.1b2 -> 3.2.1 ( #50284 )
...
This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/
2018-11-13 15:43:44 +01:00
R. RyanTM
37f01d5bf8
igv: 2.4.14 -> 2.4.15 ( #50087 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
2018-11-09 22:42:04 -05:00
royneary
bb2bae6986
mosdeph: fix compilation with nim 0.19
2018-10-31 22:03:27 +01:00
R. RyanTM
c759273e2e
star: 2.6.1a -> 2.6.1c
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
2018-10-24 15:22:22 +02:00
R. RyanTM
269efba0aa
bowtie2: 2.3.4.2 -> 2.3.4.3
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
2018-10-03 21:49:10 -07:00
R. RyanTM
77f8e10fed
picard-tools: 2.18.12 -> 2.18.14 ( #46978 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2018-09-29 21:03:17 +02:00
Orivej Desh
7545b7dcf3
platypus: 2017-03-07 -> 2018-07-22
2018-09-21 22:42:28 +00:00
Orivej Desh
cefd38b721
samtools: 1.8 -> 1.9
2018-09-21 22:42:28 +00:00
Markus J. Ankenbrand
e2df8e7c0f
seaview: init at 4.7 ( #46595 )
2018-09-13 14:10:44 +02:00
R. RyanTM
c4e8db3de0
star: 2.6.0c -> 2.6.1a ( #46176 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
star
2018-09-12 22:49:12 +02:00
Matthew Bauer
40d19d8e7c
Merge pull request #45102 from jbedo/hisat2
...
hisat2: init 2.1.0
2018-09-10 15:11:58 -05:00
R. RyanTM
f72cba212c
picard-tools: 2.18.11 -> 2.18.12
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
2018-09-06 14:22:26 -07:00
xeji
6216f5da04
Merge pull request #45263 from r-ryantm/auto-update/bowtie2
...
bowtie2: 2.3.4.1 -> 2.3.4.2
2018-08-21 19:51:36 +02:00
Uli Baum
c47aafde87
bowtie2: broken on aarch64
...
never built as far back as hydra logs go.
2018-08-21 19:11:37 +02:00
Joachim F
6755ab8b34
Merge pull request #44250 from jbedo/strelka
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strelka: init 2.9.5
2018-08-20 06:24:15 +00:00
Justin Bedo
27960b6acf
strelka: init 2.9.5
2018-08-20 08:58:22 +10:00
Vladimír Čunát
209730208a
Merge branch 'staging-next'
2018-08-17 20:51:31 +02:00
R. RyanTM
73f1448a1f
bowtie2: 2.3.4.1 -> 2.3.4.2
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions .
2018-08-17 06:50:10 -07:00
Justin Bedo
9bd7a4f520
hisat2: init 2.1.0
2018-08-17 23:03:42 +10:00
Vladimír Čunát
cbabebcc2e
Merge branch 'master' into staging-next
...
Hydra: ?compare=1473892
2018-08-17 13:45:21 +02:00
Jörg Thalheim
0359c5eb65
Merge pull request #45217 from r-ryantm/auto-update/igv
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igv: 2.4.13 -> 2.4.14
2018-08-17 11:56:26 +01:00
R. RyanTM
33ebfbfcf8
igv: 2.4.13 -> 2.4.14
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions .
2018-08-17 01:23:03 -07:00
R. RyanTM
ff7d82d405
picard-tools: 2.18.10 -> 2.18.11
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions .
2018-08-16 14:33:38 -07:00
Vladimír Čunát
5b0398dc36
Merge branch 'master' into staging-next
...
Conflicts: gobby and libinfinity - I took the hand-edited versions
instead of those resuting from the mass-replacement.
Hydra: ?compare=1473190
2018-08-13 20:43:59 +02:00
R. RyanTM
f5f55e4727
vcftools: 0.1.15 -> 0.1.16
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions .
2018-08-08 00:48:04 -07:00
Tuomas Tynkkynen
008fd5fcf5
Merge remote-tracking branch 'upstream/master' into staging
2018-08-04 15:17:42 +03:00
John Ericson
db965063b3
treewide: Make configureFlags lists
2018-08-03 17:06:03 -04:00
Uli Baum
052e4baf0a
somatic-sniper: disable parallel building
...
to fix non-deterministic failure
2018-08-03 08:27:41 +02:00
Justin Bedő
51fc0ef8d2
somatic-sniper: init 1.0.5.0 ( #43403 )
2018-08-01 22:11:13 +02:00
R. RyanTM
d7c3926352
bcftools: 1.8 -> 1.9 ( #43950 )
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/bcftools/versions .
2018-07-30 22:36:27 +02:00
Frederik Rietdijk
5dcb1febac
Merge pull request #43913 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.18.9 -> 2.18.10
2018-07-22 08:42:32 +02:00
R. RyanTM
668047ca55
picard-tools: 2.18.9 -> 2.18.10
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/picard-tools/versions .
2018-07-21 12:28:41 -07:00
volth
52f53c69ce
pkgs/*: remove unreferenced function arguments
2018-07-21 02:48:04 +00:00
R. RyanTM
ab535c2757
igv: 2.4.11 -> 2.4.13
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/igv/versions .
2018-07-13 02:49:22 -07:00
R. RyanTM
6ec4be7ec5
igv: 2.4.10 -> 2.4.11 ( #43003 )
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/igv/versions .
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11/bin/igv had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.4.11 with grep in /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11
- directory tree listing: https://gist.github.com/ca4cf484aab1c1590806c47c4fdde1d7
- du listing: https://gist.github.com/f7ff80a2429cf0a942195db4944659b1
2018-07-09 16:02:34 +02:00
Silvan Mosberger
8e2c3b93ba
Merge pull request #43096 from jbedo/mosdepth
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mosdepth: init 0.2.3
2018-07-09 04:55:24 +02:00
Justin Bedo
59141de608
mosdepth: init 0.2.3
2018-07-09 08:51:49 +10:00
R. RyanTM
cb85999b6b
picard-tools: 2.18.7 -> 2.18.9 ( #42967 )
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/picard-tools/versions .
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
2018-07-06 20:24:57 +02:00
Matthew Bauer
574883f665
Merge pull request #42571 from iimog/hmmer
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hmmer: init at 3.1b2
2018-06-28 22:00:09 -04:00
Silvan Mosberger
57bccb3cb8
treewide: http -> https sources ( #42676 )
...
* treewide: http -> https sources
This updates the source urls of all top-level packages from http to
https where possible.
* buildtorrent: fix url and tab -> spaces
2018-06-28 20:43:35 +02:00
Markus Ankenbrand
851ab7f323
hmmer: init at 3.1b2
2018-06-25 16:56:21 +02:00
R. RyanTM
b3052440f6
picard-tools: 2.18.5 -> 2.18.7 ( #41975 )
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/picard-tools/versions .
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.7 with grep in /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7
- directory tree listing: https://gist.github.com/a49ed5f2ff312ce6180174183901e38f
- du listing: https://gist.github.com/243f4d89d2100ef27d332e3562d5f173
2018-06-18 22:41:49 +02:00
R. RyanTM
d97f7d3b89
raxml: 8.2.11 -> 8.2.12 ( #41964 )
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/RAxML/versions .
These checks were done:
- built on NixOS
- /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12/bin/raxmlHPC-PTHREADS-SSE3 passed the binary check.
- 1 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 8.2.12 with grep in /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12
- directory tree listing: https://gist.github.com/8a2b70b299e53bfee9f18d2ab8cd5f9f
- du listing: https://gist.github.com/02803409663f19671adc6be233a327fd
2018-06-18 22:40:49 +02:00
R. RyanTM
e33eacbc1d
picard-tools: 2.18.4 -> 2.18.5
...
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/picard-tools/versions .
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.5 with grep in /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5
- directory tree listing: https://gist.github.com/1938ad634fa882d94e8d28fd1625547c
- du listing: https://gist.github.com/4b51e89646327900f6ef6f2242f5d0bd
2018-05-26 10:42:37 -07:00
Arcadio Rubio García
699fa7e953
star: 2.5.3a -> 2.6.0c ( #40518 )
2018-05-15 15:09:06 +02:00
Arcadio Rubio García
e4a2b70f91
minimap2: init at 2.10
2018-05-14 21:26:07 +01:00