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211 Commits

Author SHA1 Message Date
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
Ryan Bernstein
941014ffff bowtie2: init at 2.3.3.1 2017-10-22 00:11:49 +02:00
Orivej Desh
047c576353 Merge pull request #29963 from mimadrid/update/samtools-1.6.0 
samtools: 1.5.0 -> 1.6.0
 2017-10-02 01:07:11 +00:00
Orivej Desh
d73bd7f50a bcftools: fix up 2017-10-01 07:45:19 +00:00
Orivej Desh
09a5396982 samtools: fix up 2017-10-01 07:36:30 +00:00
mimadrid
bebccf176e
bcftools: 1.5.0 -> 1.6.0 2017-09-30 22:22:25 +02:00
mimadrid
ee2c76693e
samtools: 1.5.0 -> 1.6.0 2017-09-30 22:20:02 +02:00
Robin Gloster
7cbf3a27de freebayes: clean up build 2017-09-28 00:54:01 +02:00
Samuel Leathers
a3e2ecd7f7 freebayes: 1.1.0 -> 2017-08-23 2017-09-28 00:54:01 +02:00
Tuomas Tynkkynen
4b4bfbf3e5 darwin: Disable another bunch of packages never having built successfully 
tecoc: https://hydra.nixos.org/build/61141995
shallot: https://hydra.nixos.org/build/61145497
plink-ng: https://hydra.nixos.org/build/61130149
tshark: https://hydra.nixos.org/build/61479600
 2017-09-22 19:49:57 +03:00
Ben Darwin
c7bbe471b0 ants: bump version and fix sandboxed build 2017-09-20 18:42:34 -04:00
Robin Gloster
a0967948d9
bwa: 0.7.15 -> 0.7.16a 2017-09-05 14:42:45 +02:00
Samuel Leathers
d9cd226a6d neuron: 7.4 -> 7.5 2017-09-02 16:58:14 -04:00
Ryan Bernstein
749e702a46 poretools: version number to commit date 2017-08-18 09:59:26 -04:00
Ryan Bernstein
a13e4ad1f5 poretools: init at 0.6.0 2017-08-17 11:17:30 -04:00
mimadrid
15a99ae367
bcftools: 1.4.0 -> 1.5.0 2017-08-13 00:17:48 +02:00
mimadrid
ca45a26ec3
samtools: 1.4.0 -> 1.5.0 2017-08-13 00:17:25 +02:00
Silvan Mosberger
f5fa5fa4d6 pkgs: refactor needless quoting of homepage meta attribute (#27809) 
* pkgs: refactor needless quoting of homepage meta attribute

A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.

* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit

* Fixed some instances
 2017-08-01 22:03:30 +02:00
mimadrid
20fb18bdbc
igv: 2.3.89 -> 2.3.98 2017-08-01 20:46:31 +02:00
Shea Levy
24c59a4452 neuron: enable GUI 2017-06-28 11:59:54 -04:00
Justin Bedo
94ec54598c
snpeff: 4.3i -> 4.3p 2017-06-13 15:31:52 +10:00
Jörg Thalheim
be19ad150c Merge pull request #25594 from mimadrid/update/htslib-1.4 
Update/htslib 1.4
 2017-05-11 07:08:56 +01:00
mimadrid
8d1bebf83c
bcftools: 1.3.1 -> 1.4 2017-05-11 07:04:33 +01:00
mimadrid
9073e67568
samtools: 1.3.1 -> 1.4 2017-05-07 23:15:48 +02:00
Aneesh Agrawal
bd9246b009 treewide: Always use integers for meta.priority 
Meta attributes types are now enforce as of commit
90b9719f4f,
so ensure meta.priority is always set to an integer.

This fixes evaluation of `linuxPackages_latest.virtualbox`
(the impetus for this commit)
and other packages that use lowPrio or hiPrio.
 2017-05-02 01:43:22 -04:00
Michael Raskin
7ef99bf054 Merge pull request #24085 from bcdarwin/ants 
ants: set $ANTSPATH variable in shell scripts
 2017-04-30 23:03:06 +02:00
Matthias Beyer
6239da6ade diamond: init at 0.8.36 2017-04-12 13:05:57 +02:00
Justin Bedő
c5015b77af platypus: fix platforms metadata (#24666) 2017-04-06 10:10:54 +01:00
Robin Gloster
b9948fedc6
ncbi_tools: mark as broken and remove -fPIC 
PIC is used by default since 16.09
 2017-03-30 16:23:34 +02:00
Ben Darwin
fbc9a4d7dc ants: set $ANTSPATH variable in shell scripts 2017-03-22 16:01:05 -04:00
Franz Pletz
bfb7890fa0 Merge pull request #24191 from jbedo/bedtools 
bedtools: fix clang build
 2017-03-22 15:30:19 +01:00
Justin Bedo
56aeb271c9
bedtools: fix clang build 2017-03-22 12:00:24 +11:00
Dan Peebles
7ad3fd7ca7 neuron: fix on clang 3.8 and above 
This is in preparation for upgrading Darwin stdenv to LLVM 4
 2017-03-21 01:00:18 -04:00
Michael Raskin
4d5f33deff Merge pull request #23376 from bcdarwin/ants 
ANTs: init at 2.1.0 (0gyys1lf) and update ITK accordingly
 2017-03-18 18:42:24 +01:00
Robin Gloster
e2a13af49c
emboss: fix build 2017-03-13 13:15:51 +01:00
Justin Bedo
1ac797861b
SnpEff: init at 4.3i 2017-03-08 22:43:50 +01:00
Justin Bedo
076e513b94
varscan: init at 2.4.2 2017-03-08 22:43:49 +01:00
Justin Bedo
4bb50fd08c
picard-tools: init at 2.7.1 2017-03-08 22:43:45 +01:00
Justin Bedo
7f214e6410
bedtools: init at 2.26.0 2017-03-08 22:36:29 +01:00
Justin Bedo
661048c803
platypus: init at 2017-03-07 2017-03-08 22:36:03 +01:00