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350 commits

Author SHA1 Message Date
John Ericson 4ccb74011f Merge commit '18aa59b0f26fc707e7313f8467e67159e61600c2' from master into staging 
There was one conflict in the NixOS manual; I checked that it still
built after resolving it.
 2019-04-01 00:40:03 -04:00
markuskowa c637aeff19
Merge pull request #58541 from luispedro/add_megahit 
megahit: init at 1.1.4
 2019-03-31 12:51:59 +02:00
Luis Pedro Coelho bf48451959 megahit: init at 1.1.4 
This is widely used in bioinformatics for assembling genomes &
metagenomes
 2019-03-31 05:56:14 +02:00
R. RyanTM 893abe12e8 bowtie2: 2.3.4.3 -> 2.3.5 (#58014) 
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
 2019-03-31 00:37:38 +01:00
R. RyanTM 2ce544a8b1 minimap2: 2.15 -> 2.16 (#57319) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
 2019-03-27 23:25:52 +01:00
R. RyanTM 1b73fd1954 paml: 4.9h -> 4.9i (#57354) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/paml/versions
 2019-03-27 15:44:21 +01:00
Bruno Bzeznik 00431493c0 itsx: init at 1.1.1 2019-03-26 15:52:35 +01:00
Bruno Bzeznik 6858d0fd62 clustal-omega: init at 1.2.4 2019-03-26 15:45:59 +01:00
Joachim F c9cd1356ea
Merge pull request #56522 from bzizou/messer-slim 
messer-slim: init at 3.2.1
 2019-03-26 00:42:58 +00:00
Wael M. Nasreddine 5af0780492
Merge remote-tracking branch 'origin/master' into staging 
* origin/master: (693 commits)
  buildGoModule: use go_1_12 instead of go_1_11 (#58103)
  gitAndTools.lab: 0.15.2 -> 0.15.3 (#58091)
  signal-desktop: 1.22.0 -> 1.23.0
  added missing semicolon to documentation
  terminus_font_ttf: 4.46.0 -> 4.47.0
  buildGoModule: remove SSL env vars in favor of cacert in buildInputs (#58071)
  dav1d: init at 0.2.1
  dropbox-cli: 2018.11.28 -> 2019.02.14
  atlassian-confluence: 6.14.1 -> 6.14.2
  maintainers: update email for dywedir
  python.pkgs.hglib: use patch to specify hg path (#57926)
  chkrootkit: 0.52 -> 0.53
  radare2-cutter: 1.7.2 -> 1.8.0
  autorandr: 1.7 -> 1.8
  pythonPackages.pyhepmc: fix build
  llvm-polly/clang-polly: use latest llvm
  apulse: 0.1.11.1 -> 0.1.12, cleanup
  factorio: experimental 0.17.14 → 0.17.16 (#58000)
  sequeler: 0.6.7 -> 0.6.8
  nasc: 0.5.1 -> 0.5.2
  ...
 2019-03-21 21:01:25 -07:00
Matthew Bauer 37eba81c7b
Merge pull request #56391 from matthewbauer/cmake-treewide 
Add more CMake flags
 2019-03-11 12:43:46 -04:00
Matthew Bauer 6ed49262f5 treewide: remove BUILD_TESTING flag 
This is now set by CMake
 2019-03-11 10:11:28 -04:00
R. RyanTM 70815de29c picard-tools: 2.18.25 -> 2.18.27 
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
 2019-03-11 03:37:34 -07:00
R. RyanTM 27e05d81a5 star: 2.7.0a -> 2.7.0c 
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
 2019-03-03 20:55:25 +01:00
R. RyanTM 9989b7c8c4 igv: 2.4.17 -> 2.4.19 
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
 2019-03-03 20:48:52 +01:00
Bruno Bzeznik 598f11862c messer-slim: init at 3.2.1 2019-02-28 15:11:18 +01:00
tbenst 1cb81a69a0 cmtk: init at 3.3.1 (#54016) 
* cmtk: init at 3.3.1
 2019-02-08 17:41:14 -05:00
markuskowa 0496c08afd
Merge pull request #55298 from r-ryantm/auto-update/igv 
igv: 2.4.16 -> 2.4.17
 2019-02-06 12:50:24 +01:00
R. RyanTM da628f0cbd igv: 2.4.16 -> 2.4.17 
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
 2019-02-05 20:06:55 -08:00
R. RyanTM e27eaf6111 star: 2.6.1d -> 2.7.0a 
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
 2019-02-03 17:20:27 -08:00
markuskowa e27e114803
Merge pull request #53677 from jbedo/snpeff-4.3T 
snpeff: 4.3q -> 4.3t
 2019-01-31 10:36:32 +01:00
Justin Bedo 75dd587793
snpeff: 4.3q -> 4.3t 2019-01-31 15:15:05 +11:00
R. RyanTM 2b39f17d08 minimap2: 2.14 -> 2.15 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
 2019-01-28 20:01:47 +00:00
R. RyanTM 00cdff318a picard-tools: 2.18.23 -> 2.18.25 
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
 2019-01-28 17:17:30 +00:00
R. RyanTM b2a7ef628a picard-tools: 2.18.21 -> 2.18.23 
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
 2019-01-16 21:43:19 -08:00
R. RyanTM 26b492b207 minimap2: 2.10 -> 2.14 (#52845) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
 2019-01-13 22:34:45 +01:00
tbenst d34f2b9b96 bftools: init at 5.9.2 (#53769) 2019-01-10 18:28:28 -05:00
Frederik Rietdijk 2da31b80bb Merge master into staging-next 2019-01-03 20:07:35 +01:00
R. RyanTM c00dbcb7c4 picard-tools: 2.18.20 -> 2.18.21 
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
 2019-01-03 08:39:10 +01:00
Frederik Rietdijk 10afccf145 Merge staging-next into staging 2018-12-27 18:11:34 +01:00
R. RyanTM 338cf1a7fc igv: 2.4.15 -> 2.4.16 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
 2018-12-26 10:44:01 +01:00
Jan Tojnar ef935fa101
Merge branch 'master' into staging 2018-12-24 15:02:29 +01:00
Renaud 6f5ec9d889
Merge pull request #52134 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.17 -> 2.18.20
 2018-12-19 17:53:47 +01:00
Frederik Rietdijk 9ab61ab8e2 Merge staging-next into staging 2018-12-19 09:00:36 +01:00
volth fed7914539
Merge branch 'staging' into make-perl-pathd 2018-12-18 17:13:27 +00:00
markuskowa 96b0a38f07
Merge pull request #52015 from r-ryantm/auto-update/star 
star: 2.6.1c -> 2.6.1d
 2018-12-16 23:38:37 +01:00
volth bb9557eb7c lib.makePerlPath -> perlPackages.makePerlPath 2018-12-15 03:50:31 +00:00
R. RyanTM b261fb0474 picard-tools: 2.18.17 -> 2.18.20 
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
 2018-12-14 16:27:07 -08:00
R. RyanTM 87481c2ff1 star: 2.6.1c -> 2.6.1d 
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
 2018-12-14 01:07:34 -08:00
Maximilian Bosch de02111a51
Merge pull request #51534 from jbedo/bowtie2 
bowtie2: fix missing dependencies
 2018-12-10 00:58:51 +01:00
Justin Bedo 8c5251e3c0
bowtie2: fix missing dependencies 2018-12-05 10:51:30 +11:00
Frederik Rietdijk 9b81c7e455 Merge staging-next into staging 2018-11-29 09:18:35 +01:00
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
Matthew Bauer d492f53faf
Merge pull request #50527 from matthewbauer/ninja-check-phase 
Add check phase to ninja setup hook
 2018-11-20 16:55:12 -06:00
Matthew Bauer 2c47a4229f treewide: remove ctest usages 
These are already in the generated makefiles!
 2018-11-18 19:31:02 -06:00
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 
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 
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 
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 
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 
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
R. RyanTM 47c672b4b1 picard-tools: 2.18.3 -> 2.18.4 
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 binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.4 with grep in /nix/store/k62ym9i08d0w9sgmdjjfyy4lf2n9ig7p-picard-tools-2.18.4
- directory tree listing: https://gist.github.com/4d9e3062e701681d9b53033dc9511663
 2018-05-12 13:58:09 +02:00
Matthew Justin Bauer a733bbfb07
Merge pull request #39740 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.2 -> 2.18.3
 2018-05-04 17:21:50 -05:00
R. RyanTM ef01f17c2d paml: 4.9g -> 4.9h 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/paml/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 -h’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 --help’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 help’ got 0 exit code
- found 4.9h with grep in /nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h
- directory tree listing: https://gist.github.com/b2a37e7cd2b4b41178f0698f3aac69e2
 2018-05-03 15:13:15 +02:00
R. RyanTM 4ea3841d7f picard-tools: 2.18.2 -> 2.18.3 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.3 with grep in /nix/store/q67hqz7716nf3c4f8rjmlpf2dqbb06rz-picard-tools-2.18.3
- directory tree listing: https://gist.github.com/6b71ce718f18ef6a48c05457cd0e583b
 2018-04-30 11:43:21 -07:00
Ben Darwin fa850e8fda conglomerate: init at 2017-09-10 2018-04-27 18:57:17 -04:00
Jörg Thalheim f7785dd61c
Merge branch 'master' into minc_ecosystem 2018-04-21 20:18:27 +01:00
Jörg Thalheim 39e94277ba
Merge pull request #39197 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.1 -> 2.18.2
 2018-04-21 19:21:15 +01:00
R. RyanTM 7d22bbe671 picard-tools: 2.18.1 -> 2.18.2 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.2 with grep in /nix/store/sp6gc6c6knpvpsmfdx8074qclcsgs931-picard-tools-2.18.2
- directory tree listing: https://gist.github.com/114857d15222eccda94501b5a871fb24
 2018-04-20 00:44:45 -07:00
R. RyanTM c478b6217f samtools: 1.7 -> 1.8 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/samtools/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
- found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
- directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2
 2018-04-10 13:04:09 -07:00
Ben Darwin de2f36982b ezminc: init at 2017-08-29 2018-04-09 18:07:15 -04:00
Ben Darwin cf2aac6a04 address license/version issues for PR #29782 2018-04-09 18:06:54 -04:00
Ben Darwin e90d1e8631 inormalize: init at 1.0.20 (develop branch) 2018-04-09 18:06:54 -04:00
Ben Darwin 54c543b03b n3: init at 1.0.20 2018-04-09 18:06:54 -04:00
Ben Darwin f532f9f5f4 minc-widgets: init at "1.0.0" (package seems to lack a consistent version) 2018-04-09 18:06:33 -04:00
Ben Darwin bd460f54a3 mni_autoreg: init at 0.99.70 2018-04-09 18:06:33 -04:00
Ben Darwin 082b3f1058 minc-tools: 2.3.00 -> 2.3.01 (develop branch) 2018-04-09 18:06:33 -04:00
Matthew Justin Bauer 209dce5ada
Merge pull request #38165 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.17.11 -> 2.18.1
 2018-04-08 21:21:14 -05:00
Jörg Thalheim 18fa54032a bcftools: python/perl is needed for shebangs 2018-04-08 09:35:20 +01:00
R. RyanTM 7b75bc79ef bcftools: 1.7 -> 1.8 
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.

These checks were done:

- built on NixOS
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools help’ got 0 exit code
- found 1.8 with grep in /nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8
- directory tree listing: https://gist.github.com/c9ddd760c0c740dabaabeb604fbb8a5a
 2018-04-07 20:11:48 -07:00
R. RyanTM 34257096e6 igv: 2.4.9 -> 2.4.10 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/igv/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.4.10 with grep in /nix/store/171fy8d969ynn0m74xi7dxvrbv9di37z-igv-2.4.10
- directory tree listing: https://gist.github.com/9164cca651385e7845f2ac52628d5ad7
 2018-03-31 08:54:46 -07:00
R. RyanTM d5f23bb90a picard-tools: 2.17.11 -> 2.18.1 
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 binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.1 with grep in /nix/store/nxd67d6cdp85kjy0g2qg4005rbwdfj75-picard-tools-2.18.1
- directory tree listing: https://gist.github.com/2fdec4f7617ad9bc0dfcd95a91d4abb6
 2018-03-30 20:27:46 -07:00
Matthew Justin Bauer 964c32bcb3
Merge pull request #36846 from jbedo/snpeff 
snpeff: 4.3t -> 4.3q
 2018-03-19 12:26:33 -05:00
Matthew Justin Bauer 9f58d17d10
Merge pull request #37079 from ryantm/auto-update/picard-tools 
picard-tools: 2.17.10 -> 2.17.11
 2018-03-19 04:04:50 -05:00
Gabriel Ebner 5df4f227ec
Merge pull request #37009 from ryantm/auto-update/igv 
igv: 2.4.8 -> 2.4.9
 2018-03-17 13:43:23 +01:00
Ryan Mulligan 892244dda0 picard-tools: 2.17.10 -> 2.17.11 
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.17.11 with grep in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
- found 2.17.11 in filename of file in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
 2018-03-15 01:16:28 -07:00
Ryan Mulligan 9b4c82d366 igv: 2.4.8 -> 2.4.9 
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.4.9 with grep in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
- found 2.4.9 in filename of file in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
 2018-03-14 12:04:23 -07:00
Justin Bedo f48ff649fe
snpeff: 4.3t -> 4.3q 2018-03-12 16:03:44 +11:00
Ryan Mulligan 49272f60dd paml: 4.9c -> 4.9g 
Semi-automatic update. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 4.9g in filename of file in /nix/store/70p59yxnlzhbj8ig1ax8lrrsdbcf37zp-paml-4.9g
 2018-03-09 07:22:27 -08:00
Ryan Mulligan 0c69b50356 picard-tools: 2.17.4 -> 2.17.10 
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.17.10 with grep in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10
- found 2.17.10 in filename of file in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10

cc "@jbedo"
 2018-02-28 15:02:46 +00:00
Ryan Mulligan d1dc4cae54 igv: 2.4.6 -> 2.4.8 
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.4.8 with grep in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8
- found 2.4.8 in filename of file in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8

cc "@mimadrid"
 2018-02-26 19:11:52 -08:00
adisbladis e046d8bc08
Merge pull request #35555 from ryantm/auto-update/bcftools-1.6-to-1.7 
bcftools: 1.6 -> 1.7
 2018-02-26 17:39:46 +08:00
Ryan Mulligan bc730862d5 bowtie2: 2.3.4 -> 2.3.4.1 
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` and found version 2.3.4.1
- found 2.3.4.1 with grep in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
- found 2.3.4.1 in filename of file in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
 2018-02-25 09:45:04 -08:00
Ryan Mulligan 9af7602b8a bcftools: 1.6 -> 1.7 
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -v` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats --help` got 0 exit code
- found 1.7 with grep in /nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7
 2018-02-25 09:02:06 -08:00
Jörg Thalheim 08d1400816
Merge pull request #34530 from unode/samtools-old 
samtools-old: init at 0.1.19
 2018-02-10 08:34:26 +00:00
Jörg Thalheim 80b096b2b3
Merge pull request #34531 from unode/raxml 
RAxML: init at 8.2.11 (SSE3 & MPI)
 2018-02-10 08:32:19 +00:00
Renato Alves 154d1d2f19
samtools: 1.6 -> 1.7 2018-02-06 15:38:00 +01:00
Renato Alves 65ea5f8857
samtools_0_1_19: init at 0.1.19 
samtools-1.5 already exists but some software requires the older version
 2018-02-02 21:49:50 +01:00
Renato Alves 05889c52b9
RAxML: init at 8.2.11 (SSE3 & MPI) 
This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
 2018-02-02 18:31:40 +01:00
Renato Alves b22e4976cb
muscle: init at 3.8.31 2018-01-28 12:32:46 +01:00
Alexey Shmalko 38fbc93f46
Merge pull request #34156 from arcadio/star 
star: init at 2.5.3a
 2018-01-27 17:02:16 +02:00
adisbladis 7a2d35d9db
Merge pull request #34119 from arcadio/master 
igv: 2.3.98 -> 2.4.6
 2018-01-25 18:33:49 +08:00
Samuel Leathers efdb0983da
Merge pull request #34199 from arcadio/kallisto 
kallisto: init at 0.43.1
 2018-01-24 20:43:24 -07:00
Arcadio Rubio García a7333e9ced kallisto: init at 0.43.1 2018-01-24 16:16:46 +00:00
Arcadio Rubio García 72d675b23c star: init at 2.5.3a 2018-01-24 16:07:15 +00:00
adisbladis 266979a360
Merge pull request #34125 from arcadio/bwa 
bwa: 0.7.16a -> 0.7.17
 2018-01-23 20:12:56 +08:00
adisbladis b0603f514b
Merge pull request #34139 from arcadio/bedtools 
bedtools: 2.26.0 -> 2.27.1
 2018-01-23 12:56:01 +08:00
adisbladis 7490d4d698
Merge pull request #34140 from arcadio/picard 
picard-tools: 2.7.1 -> 2.17.4
 2018-01-22 23:57:10 +08:00
Arcadio Rubio García 612953567d bowtie2: 2.3.3.1 -> 2.3.4 2018-01-22 12:28:06 +00:00
Arcadio Rubio García 12c5dc343f picard-tools: 2.7.1 -> 2.17.4 2018-01-22 12:16:26 +00:00
Arcadio Rubio García c75e91a374 bedtools: 2.26.0 -> 2.27.1 2018-01-22 12:09:44 +00:00
Arcadio Rubio García 0d05bcae8c bwa: 0.7.16a -> 0.7.17 2018-01-22 01:58:36 +00:00
Arcadio Rubio García 550e6146d4 igv: 2.3.98 -> 2.4.6 2018-01-21 21:07:44 +00:00
Ashley Gillman 245a67df8b dcm2niix: cmake is native, style 2018-01-15 16:53:28 +10:00
Ashley Gillman 271d4a7ca0 dcm2niix: init at 1.0.20170130 2018-01-15 16:45:03 +10:00
Justin Bedo a49c91f655
snpeff: 4.3p -> 4.3t 2017-12-21 10:52:26 +11:00
Orivej Desh 1f99fd6965 libminc: fix build after hdf5 upgrade by using hdf5_1_8 2017-12-01 00:37:29 +00:00
rybern ef0486b1f9 vcftools: init at 0.1.15 (#31339) 2017-11-16 09:52:56 +02:00