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1722 commits

Author SHA1 Message Date
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
Matthew Justin Bauer 0d8e415d6b
Merge pull request #38969 from vbgl/coq-findlib 
coq: fix installation of OCaml libraries
 2018-04-20 18:02:52 -05:00
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
xeji b3d50c7afa shogun: disable paralllel building 
... to avoid sporadic failures
 2018-04-19 12:27:00 -05:00
Matthew Justin Bauer 1bb28f26e8
Merge pull request #38810 from timokau/giac-improvements 
giac: enable checks, separate outputs
 2018-04-19 12:03:53 -05:00
Timo Kaufmann ddb7c0e930 lrcalc: init at 1.2 (#38755) 2018-04-19 08:42:06 +02:00
Matthew Justin Bauer 853529b2ea
Merge pull request #38740 from r-ryantm/auto-update/cytoscape 
cytoscape: 3.6.0 -> 3.6.1
 2018-04-18 22:20:04 -05:00
Vincent Laporte 76a43d765c coq: 8.8+beta1 -> 8.8.0 2018-04-18 14:37:04 +02:00
Matthew Justin Bauer 88098d58f2
Merge pull request #38701 from r-ryantm/auto-update/samtools 
samtools: 1.7 -> 1.8
 2018-04-17 12:03:42 -05:00
Matthew Justin Bauer 1ec5b0389d
Merge pull request #36582 from ryantm/auto-update/gromacs 
gromacs: 4.6.7 -> 2018
 2018-04-17 10:38:06 -05:00
Jörg Thalheim 5dc7a70f65
Merge pull request #38589 from badi/tlatools 
Add TLAPS and TLA+ Toolbox
 2018-04-17 14:51:35 +01:00
Vladimír Čunát db071c4d1d
Merge #38702: Mark packages as broken (ZHF) 2018-04-17 13:36:20 +02:00
Badi Abdul-Wahid c4ef846c92
tlaplusToolbox: init at 1.5.6 2018-04-16 22:18:47 -04:00
Badi Abdul-Wahid d14a476054
tlaps: init at 1.4.3 2018-04-16 21:18:42 -04:00
Vincent Laporte dc4a8435f0
symbiyosys: larger meta.platforms 2018-04-16 11:47:48 +00:00
Jan Tojnar cee2c50748
celestia: clean up 2018-04-15 17:21:23 +02:00
Vincent Laporte caec7dbb9f
coq: fix installation of OCaml libraries 2018-04-15 11:24:17 +00:00
Vincent Laporte 5f97adccdc
coq: move some attributes inside passthru 2018-04-15 11:24:17 +00:00
Gabriel Ebner 9df0c12cde elan: 0.3.0 -> 0.3.2 2018-04-13 09:28:28 +02:00
xeji 6866542751 torchPackages.{sundown,lbase64}: mark as broken 2018-04-12 23:04:04 +02:00
xeji d63702a473 openmvg: mark as broken 2018-04-12 23:04:02 +02:00
Michael Raskin 783204bdbc
Merge pull request #38768 from timokau/singular-4.1.1 
singular: 3.1.7 -> 4.1.1
 2018-04-12 11:40:06 +00:00
Peter Simons 722d8226f4
Merge pull request #38812 from timokau/maxima-ecl 
maxima: add various fixes, re-add ecl support
 2018-04-12 11:43:15 +02:00
Timo Kaufmann eb119b045a maxima: add various fixes, re-add ecl support 2018-04-12 00:46:40 +02:00
Timo Kaufmann 32cf225ad9 giac: enable checks, separate outputs 2018-04-11 22:56:21 +02:00
Gabriel Ebner 99ee7fd311 elan: add leanchecker proxy 2018-04-11 19:08:22 +02:00
Gabriel Ebner a378389ac2 elan: 0.1.0 -> 0.3.0 2018-04-11 18:05:15 +02:00
Guillaume Maudoux b7dbff3aac gap-minimal: fix ofBorg evaluation 2018-04-11 17:08:54 +02:00
Timo Kaufmann fa3d0cef67 singular: 3.1.7 -> 4.1.1 2018-04-11 17:00:20 +02:00
Timo Kaufmann 6dc287802a gap: 4r8p3 -> 4r8p10 2018-04-11 15:22:03 +02:00
R. RyanTM 65e18bd38f cytoscape: 3.6.0 -> 3.6.1 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

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

These checks were done:

- built on NixOS
- ran ‘/nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1/bin/cytoscape -h’ got 0 exit code
- ran ‘/nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1/bin/cytoscape --help’ got 0 exit code
- found 3.6.1 with grep in /nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1
- directory tree listing: https://gist.github.com/8bad808238fc034c5394a80d8a5c1554
 2018-04-11 01:12:34 -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
Gabriel Ebner a14ae55c04 elan: init at 0.1.0 2018-04-10 18:38:45 +02:00
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 6a74718e00
Merge pull request #36852 from rprospero/sasview-for-pr 
sasview: init at 4.1.2
 2018-04-09 14:07:40 -05:00
Matthew Justin Bauer 72a54f3b6d
Merge pull request #38260 from symphorien/tamarin-vim 
tamarin-prover: install vim syntax highlighting files
 2018-04-08 21:47:12 -05:00
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 1e9e19b2aa openmvs-unstable: 2017-05-01 -> 2018-05-26 
fix build
 2018-04-08 10:36:25 +01:00
Jörg Thalheim 62dc989963
Merge pull request #38595 from r-ryantm/auto-update/bcftools 
bcftools: 1.7 -> 1.8
 2018-04-08 09:36:13 +01:00
Jörg Thalheim 18fa54032a bcftools: python/perl is needed for shebangs 2018-04-08 09:35:20 +01:00
Austin Seipp 86c5420a2e nixpkgs: remove z3 4.5.0 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-04-07 23:02:59 -05:00
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
Jörg Thalheim d307ab5ca3
Merge pull request #38416 from bcdarwin/beluga 
beluga: init at 20180403
 2018-04-06 00:34:47 +01:00