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Author SHA1 Message Date
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
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 
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 
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 
- 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 
gcc not available
 2016-08-10 22:48:19 -05:00
Tuomas Tynkkynen f87f37c1ee bwa: Broken on i686 
http://hydra.nixos.org/build/38236956
 2016-08-06 17:06:45 +03:00
Tuomas Tynkkynen 21f17d69f6 treewide: Add lots of meta.platforms 
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 
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 
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 
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 
(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