JakeHillion/nixpkgs
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23 Commits

Author SHA1 Message Date
Luis Pedro Coelho
5877d8e072 samtools: Fix cross-compilation 
Tests require bgzip which comes from the htslib package.

This did not cause problems prior to
41485e7337 as tests were not run in
cross-compilation.
 2022-08-02 17:52:50 +02:00
Luis Pedro Coelho
4758873378 Static build for samtools 
Curses is not supported (it may be possible to support it)
 2022-05-04 02:16:17 +02:00
Sergei Trofimovich
8147fb683c samtools: pull upstream fix for ncurses-6.3 
Without the fix build on ncurses-6.3 fails as:

    bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
       88 |     mvprintw(y,x,str);
          |     ^~~~~~~~
 2021-11-26 13:02:05 +00:00
Justin Bedo
02a1a2b3c8
samtools: 1.11 -> 1.13 2021-10-12 10:19:36 +11:00
Ben Siraphob
badf51221d treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
Profpatsch
4a7f99d55d treewide: with stdenv.lib; in meta -> with lib; 
Part of: https://github.com/NixOS/nixpkgs/issues/108938

meta = with stdenv.lib;

is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.

This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.

The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
 2021-01-11 10:38:22 +01:00
Renato Alves
a28e5b0a4f
samtools: 1.10 -> 1.11 2020-10-29 18:27:22 +01:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
Jonathan Ringer
4de137a77d samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
Miguel Madrid Mencía
148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
volth
46420bbaa3 treewide: name -> pname (easy cases) (#66585) 
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
 2019-08-15 13:41:18 +01:00
Orivej Desh
cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
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
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
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
Orivej Desh
09a5396982 samtools: fix up 2017-10-01 07:36:30 +00:00
mimadrid
ee2c76693e
samtools: 1.5.0 -> 1.6.0 2017-09-30 22:20:02 +02:00
mimadrid
ca45a26ec3
samtools: 1.4.0 -> 1.5.0 2017-08-13 00:17:25 +02:00
mimadrid
9073e67568
samtools: 1.3.1 -> 1.4 2017-05-07 23:15:48 +02:00
mimadrid
14feec44e4
samtools: refactoring 2016-06-24 21:08:17 +02:00
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