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
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star: init at 2.5.3a
2018-01-27 17:02:16 +02:00
adisbladis
7a2d35d9db
Merge pull request #34119 from arcadio/master
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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
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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
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bwa: 0.7.16a -> 0.7.17
2018-01-23 20:12:56 +08:00
adisbladis
b0603f514b
Merge pull request #34139 from arcadio/bedtools
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bedtools: 2.26.0 -> 2.27.1
2018-01-23 12:56:01 +08:00
adisbladis
7490d4d698
Merge pull request #34140 from arcadio/picard
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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
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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
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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
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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
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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
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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
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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
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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
...
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
...
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
...
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