Franz Pletz
bfb7890fa0
Merge pull request #24191 from jbedo/bedtools
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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
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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
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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
Ben Darwin
05359c327b
ANTs: init at 2.1.0 (0gyys1lf)
2017-03-01 21:06:30 -05:00
Celine Mercier
78c052e91a
ecopcr: init at 0.8.0
2017-02-06 16:01:08 +01:00
Ian Lancaster
5f67b7b30a
emboss: 6.0.1 -> 6.6.0
2017-02-04 19:05:48 -05:00
mimadrid
29cb10c021
igv: 2.3.77 -> 2.3.89
2016-12-23 19:37:10 -05:00
Jason Daniel Augustine Gilliland
59ca5d213f
freebayes: init at 1.1.0
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Signed-off-by: zimbatm <zimbatm@zimbatm.com>
2016-12-22 14:10:37 +00:00
Justin Bedo
a6d6a3972f
plink-ng: init at 1.90b3
2016-11-14 20:28:39 +11:00
Justin Bedo
ec31e2cc27
Fix bcftools installation prefix
2016-11-09 08:03:04 +11:00
Tim Steinbach
6d11e8ed4c
Remove pal2nal
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No longer build/exists
2016-11-03 21:58:47 -04:00
Tim Steinbach
c36a1d6502
paml: 4.2a -> 4.9c
2016-11-03 21:33:19 -04:00
obadz
2919375c91
minc_tools: don't run tests which have been failing since first pkged
2016-09-05 17:26:12 +01:00
Adrien Devresse
28d2d78b55
neuron: fix issue with incorrectly prefixed python path
2016-09-01 13:41:26 +02:00
Frederik Rietdijk
684f08166c
fixup
2016-09-01 12:03:10 +02:00
Adrien Devresse
ae2800378f
neuron: fix issue #17914 -> Add python bindings to neuron derivation and minor fixes
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- Add support for python bindings
- make neuron respect standard pythonpath prefix
- force exec_prefix == prefix to respect standard nix file hierarchy
- normalize indentation
- propagate dependencies necessary for nrniv_makefile usage
- Add support for darwin
2016-09-01 12:03:10 +02:00
Matthew Bauer
96322f6926
bcftools: fix darwin building
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gcc not available
2016-08-10 22:48:19 -05:00
Tuomas Tynkkynen
f87f37c1ee
bwa: Broken on i686
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http://hydra.nixos.org/build/38236956
2016-08-06 17:06:45 +03:00
Tuomas Tynkkynen
21f17d69f6
treewide: Add lots of meta.platforms
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Build-tested on x86_64 Linux & Mac.
2016-08-02 21:42:43 +03:00
Tuomas Tynkkynen
102ffa6be7
treewide: Wrap some really long package descriptions
2016-08-02 21:17:44 +03:00
mimadrid
5c7a75412e
igv: init at 2.3.77
2016-06-26 19:27:56 +02:00
Joachim Fasting
46b07b335b
Merge pull request #16379 from mimadrid/init/bcftools-1.3.1
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bcftools: init at 1.3.1
2016-06-24 22:15:51 +02:00
mimadrid
d91d245f16
bcftools: init at 1.3.1
2016-06-24 21:08:17 +02:00
mimadrid
14feec44e4
samtools: refactoring
2016-06-24 21:08:17 +02:00
Luis Pedro Coelho
bd617cb185
init bwa at 0.7.15
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Closes #16064
2016-06-08 17:25:20 +01:00
Tobias Geerinckx-Rice
dce1edf946
samtools: 1.3 -> 1.3.1
2016-05-25 02:06:47 +02:00
Louis Taylor
70c1b2b1c0
samtools: init at 1.3
2016-04-12 20:13:40 +01:00
Ben Darwin
69c628e1ff
minc-tools: init at 2.3.00
2016-02-23 14:03:56 -05:00
devresse
4046d3ce8d
neuron: init at 7.4
2016-02-21 15:02:47 +00:00
Tobias Geerinckx-Rice
7b6d9d4cff
Remove arb and then-orphaned lesstif93
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Arb has been broken (and marked as such) since the removal of
GCC 4.2 in July 2014. Nothing and no-one uses it. Time to go.
2015-05-26 11:46:41 +02:00
Bjørn Forsman
c9baba9212
Fix many package descriptions
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(My OCD kicked in today...)
Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.
I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.
I've tried to stay away from generated expressions (and I think I
succeeded).
Some specifics worth mentioning:
* cron, has "Vixie Cron" in its description. The "Vixie" part is not
mentioned anywhere else. I kept it in a parenthesis at the end of the
description.
* ctags description started with "Exuberant Ctags ...", and the
"exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
at the end of description.
* nix has the description "The Nix Deployment System". Since that
doesn't really say much what it is/does (especially after removing
the package name!), I changed that to "Powerful package manager that
makes package management reliable and reproducible" (borrowed from
nixos.org).
* Tons of "GNU Foo, Foo is a [the important bits]" descriptions
is changed to just [the important bits]. If the package name doesn't
contain GNU I don't think it's needed to say it in the description
either.
2014-08-24 22:31:37 +02:00
Eelco Dolstra
8a7f3c3618
Mark a bunch of packages as broken or not supported on Darwin
2014-08-08 17:59:02 +02:00
Mateusz Kowalczyk
7a45996233
Turn some license strings into lib.licenses values
2014-07-28 11:31:14 +02:00
Eelco Dolstra
6f11a6681d
arb: Mark as broken
2014-07-22 15:12:21 +02:00
Bjørn Forsman
28ac782583
Some description fixes
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There are many more packages to fix, this is just a start.
Rules:
* Don't repeat the package name (not always that easy...)
* Start with capital letter
* Don't end with full stop
* Don't start with "The ..." or "A ..."
I've also added descriptions to some packages and rewritten others.
2013-10-05 19:36:23 +02:00
Justin Bedo
c38ffa7b7d
Added expression for PLINK
2013-09-19 09:39:14 +10:00
Eelco Dolstra
5553546c21
Remove a bunch of unreferenced files
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Plus a small number of obsolete packages (like old versions of qemu).
2012-11-29 13:43:37 +01:00
Yury G. Kudryashov
75207a6a90
Try to update slr
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Still fails to build because atlas doesn't provide full blas.
svn path=/nixpkgs/trunk/; revision=33164
2012-03-16 17:15:52 +00:00
Eelco Dolstra
c556a6ea46
* "ensureDir" -> "mkdir -p". "ensureDir" is a rather pointless
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function, so obsolete it.
svn path=/nixpkgs/branches/stdenv-updates/; revision=31644
2012-01-18 20:16:00 +00:00
Eelco Dolstra
f1598a8941
* More cleanup.
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svn path=/nixpkgs/trunk/; revision=22798
2010-07-28 18:01:17 +00:00
Pjotr Prins
17e2100b03
Updated PAML package to 4.2a
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svn path=/nixpkgs/trunk/; revision=14262
2009-02-26 15:22:13 +00:00
Pjotr Prins
7ba68d934f
Added note on package status for 64 bits
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svn path=/nixpkgs/trunk/; revision=14090
2009-02-17 08:23:21 +00:00
Pjotr Prins
387a7a85d6
Updated NCBI tools to latest version
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svn path=/nixpkgs/trunk/; revision=14087
2009-02-16 16:38:55 +00:00
Pjotr Prins
3ce5cba9c7
Added pkgMaintainer info to these 'biology' section packages.
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svn path=/nixpkgs/trunk/; revision=12987
2008-10-07 15:12:06 +00:00
Pjotr Prins
b3aa5d6bfc
Added meta.pkgMaintainer to biology packages - a claim to fame, or
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you know who to blame!
svn path=/nixpkgs/trunk/; revision=12986
2008-10-07 15:12:01 +00:00
Pjotr Prins
4ab58fc7f3
Squashed commit of the following:
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commit 74c0e9192e17d9dfce50f811fdb7e82a2785134e
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:33:39 2008 +0200
Merge
commit ad91fb07a47226ed9e99f2dcb55b69ea0e70aa84
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:23:20 2008 +0200
openmotif: added some comments on license and download
commit 68a552975f5c7e0964c7c9625e08de0864757255
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:10:49 2008 +0200
Match parameters so arb starts compiling against openmotif
commit 16c52fb4071193f89acf6f7f53cfeff322285555
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:04:06 2008 +0200
Added openmotif package
commit 75c4bba418f16859e99e97f48785e27ad87e99f5
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 15:20:55 2008 +0200
Adding openmotif
commit 83a847d194b007e2ef856f2a5ad7c49939b6cf8c
Merge: 52918f1... 5ba4f06...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 14:15:05 2008 +0200
Merge branch 'syncsvn'
Conflicts:
pkgs/top-level/all-packages.nix
commit 52918f1f3af55429cc80c99d695e4a8d8b7869b0
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 18:31:06 2008 +0200
arb: Removed xfig as dependency (will add later)
arb: Don't recurse chmod settings of shared dir
commit c283733782dcbf0dcd88710e83f3eededf8f0866
Merge: e434cdf... a51773a...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 17:09:42 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit a51773a3d4295d7ce16e6a7e983ded814180e30a
Merge: 290ae0b... 241012c...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 16:54:14 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit e434cdf9b9acefab4f54e18204ff16af179c442d
Merge: ef57566... 241012c...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 16:12:27 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit 241012cae194d0f770be2224b5bb18b66e3ae0f0
Author: Pj <wrk@bio03.(none)>
Date: Mon Oct 6 16:11:11 2008 +0200
Added older version of lesstif for arb
commit 290ae0b802285a8dda41b3c5730e53239d73b47c
Merge: dfdf7fe... 53b6ceb...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 15:20:17 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit dfdf7fe8ac9599ec372bdb83630a236f227ad7d5
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 15:15:04 2008 +0200
Fixed missing parameters for arb - and added kernelHeaders_2.6.18
commit ef57566834eb786cdcb57a799b7d1cb284eee389
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 15:06:26 2008 +0200
Changed arb permissions and priority
svn path=/nixpkgs/trunk/; revision=12985
2008-10-07 14:35:11 +00:00
Pjotr Prins
bd0b84b3c7
Changed arb permissions and priority
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svn path=/nixpkgs/trunk/; revision=12969
2008-10-06 13:17:56 +00:00
Pjotr Prins
6d70506401
Small fixes to ARB
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Included older kernel headers
svn path=/nixpkgs/trunk/; revision=12961
2008-10-05 10:56:47 +00:00
Pjotr Prins
c38a72a573
Added more dependencies for ARB
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svn path=/nixpkgs/trunk/; revision=12959
2008-10-05 10:56:44 +00:00
Pjotr Prins
fcb2efbc92
Added shared dir and updated reference to ARB
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svn path=/nixpkgs/trunk/; revision=12958
2008-10-05 10:56:23 +00:00
Pjotr Prins
29d6189e8b
The arb package (biology)
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svn path=/nixpkgs/trunk/; revision=12956
2008-10-05 09:03:58 +00:00
Pjotr Prins
034f28e268
Biology package
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svn path=/nixpkgs/trunk/; revision=12953
2008-10-05 09:00:19 +00:00
Pjotr Prins
df1e47822b
Lower priority of this package because of zlib.so conflict
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svn path=/nixpkgs/trunk/; revision=12945
2008-10-05 08:42:40 +00:00
Pjotr Prins
c09e1e540c
Introduced pal2nal package
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svn path=/nixpkgs/trunk/; revision=12896
2008-09-19 13:39:17 +00:00
Pjotr Prins
301f2e3094
Bumped PAML version
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svn path=/nixpkgs/trunk/; revision=12895
2008-09-19 13:36:35 +00:00
Pjotr Prins
2a845ebb7a
Removing clustalw2 package - may come back later
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svn path=/nixpkgs/trunk/; revision=12400
2008-07-23 08:37:00 +00:00
Pjotr Prins
0014ffcbae
Updated emboss package to 6.0.1
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svn path=/nixpkgs/trunk/; revision=12399
2008-07-23 08:22:23 +00:00
Pjotr Prins
0e751ebadc
Long description
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svn path=/nixpkgs/trunk/; revision=12005
2008-06-07 06:41:18 +00:00
Pjotr Prins
289da88ccc
Moved NCBI-tools to applications
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svn path=/nixpkgs/trunk/; revision=12004
2008-06-07 06:34:02 +00:00
Pjotr Prins
f9e018c80d
biology/paml added
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svn path=/nixpkgs/trunk/; revision=11997
2008-06-06 08:23:49 +00:00
Pjotr Prins
62c9176206
Added emboss
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svn path=/nixpkgs/trunk/; revision=11993
2008-06-05 17:14:33 +00:00
Pjotr Prins
5866a8b101
tabs2spaces of .nix file
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svn path=/nixpkgs/trunk/; revision=11992
2008-06-05 16:58:41 +00:00
Pjotr Prins
13463a6f01
MrBayes - a biology package for phylogeny
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svn path=/nixpkgs/trunk/; revision=11986
2008-06-05 13:35:45 +00:00
Pjotr Prins
849e3eb21c
biology/clustalw2 package
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svn path=/nixpkgs/trunk/; revision=11631
2008-04-15 09:32:12 +00:00