···

       
1
       
1
       
-
       
{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }:

     

       
1
       
1
       
+
       
{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }:

     

       
2
       
2
       
 
       


     

       
3
       
3
       
 
       
stdenv.mkDerivation rec {

     

       
4
       
4
       
 
       
  name = "${pname}-${version}";

     

       
5
       
5
       
 
       
  pname = "bcftools";

     

       
6
       
6
       
-
       
  major = "1.5";

     

       
7
       
7
       
-
       
  version = "${major}.0";

     

       
6
       
6
       
+
       
  version = "1.6";

     

       
8
       
7
       
 
       


     

       
9
       
8
       
 
       
  src = fetchurl {

     

       
10
       
10
       
-
       
    url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2";

     

       
11
       
11
       
-
       
    sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz";

     

       
9
       
9
       
+
       
    url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2";

     

       
10
       
10
       
+
       
    sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";

     

       
12
       
11
       
 
       
  };

     

       
13
       
12
       
 
       


     

       
14
       
14
       
-
       
  buildInputs = [ zlib bzip2 lzma perl ];

     

       
13
       
13
       
+
       
  nativeBuildInputs = [ perl ];

     

       
14
       
14
       
+
       


     

       
15
       
15
       
+
       
  buildInputs = [ htslib zlib bzip2 lzma curl ];

     

       
15
       
16
       
 
       


     

       
16
       
17
       
 
       
  makeFlags = [

     

       
17
       
18
       
 
       
    "HSTDIR=${htslib}"

     

       
18
       
19
       
 
       
    "prefix=$(out)"

     

       
19
       
20
       
 
       
    "CC=cc"

     

       
20
       
21
       
 
       
  ];

     

       
22
       
22
       
+
       


     

       
23
       
23
       
+
       
  preCheck = ''

     

       
24
       
24
       
+
       
    patchShebangs misc/

     

       
25
       
25
       
+
       
    patchShebangs test/

     

       
26
       
26
       
+
       
    sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl

     

       
27
       
27
       
+
       
  '';

     

       
28
       
28
       
+
       


     

       
29
       
29
       
+
       
  enableParallelBuilding = true;

     

       
30
       
30
       
+
       


     

       
31
       
31
       
+
       
  doCheck = true;

     

       
21
       
32
       
 
       


     

       
22
       
33
       
 
       
  meta = with stdenv.lib; {

     

       
23
       
34
       
 
       
    description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";

     

···

       
1
       
1
       
-
       
{ stdenv, fetchurl, zlib, htslib,  ncurses ? null }:

     

       
1
       
1
       
+
       
{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:

     

       
2
       
2
       
 
       


     

       
3
       
3
       
 
       
stdenv.mkDerivation rec {

     

       
4
       
4
       
 
       
  name = "${pname}-${version}";

     

       
5
       
5
       
 
       
  pname = "samtools";

     

       
6
       
6
       
-
       
  major = "1.5";

     

       
7
       
7
       
-
       
  version = "${major}.0";

     

       
6
       
6
       
+
       
  version = "1.6";

     

       
8
       
7
       
 
       


     

       
9
       
8
       
 
       
  src = fetchurl {

     

       
10
       
10
       
-
       
    url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2";

     

       
11
       
11
       
-
       
    sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5";

     

       
9
       
9
       
+
       
    url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";

     

       
10
       
10
       
+
       
    sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f";

     

       
12
       
11
       
 
       
  };

     

       
13
       
12
       
 
       


     

       
14
       
14
       
-
       
  buildInputs = [ zlib ncurses ];

     

       
13
       
13
       
+
       
  nativeBuildInputs = [ perl ];

     

       
14
       
14
       
+
       


     

       
15
       
15
       
+
       
  buildInputs = [ zlib ncurses htslib ];

     

       
15
       
16
       
 
       


     

       
16
       
17
       
 
       
  configureFlags = [ "--with-htslib=${htslib}" ]

     

       
17
       
18
       
 
       
    ++ stdenv.lib.optional (ncurses == null) "--without-curses";

     

       
19
       
19
       
+
       


     

       
20
       
20
       
+
       
  preCheck = ''

     

       
21
       
21
       
+
       
    patchShebangs test/

     

       
22
       
22
       
+
       
  '';

     

       
23
       
23
       
+
       


     

       
24
       
24
       
+
       
  enableParallelBuilding = true;

     

       
25
       
25
       
+
       


     

       
26
       
26
       
+
       
  doCheck = true;

     

       
18
       
27
       
 
       


     

       
19
       
28
       
 
       
  meta = with stdenv.lib; {

     

       
20
       
29
       
 
       
    description = "Tools for manipulating SAM/BAM/CRAM format";

     

···

       
1
       
1
       
-
       
{ stdenv, fetchurl, zlib, bzip2, lzma, curl }:

     

       
1
       
1
       
+
       
{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }:

     

       
2
       
2
       
 
       


     

       
3
       
3
       
 
       
stdenv.mkDerivation rec {

     

       
4
       
4
       
 
       
  name = "${pname}-${version}";

     

       
5
       
5
       
-
       
  version = "${major}.0";

     

       
6
       
5
       
 
       
  pname = "htslib";

     

       
7
       
7
       
-
       
  major = "1.5";

     

       
6
       
6
       
+
       
  version = "1.6";

     

       
8
       
7
       
 
       


     

       
9
       
8
       
 
       
  src = fetchurl {

     

       
10
       
10
       
-
       
    url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2";

     

       
11
       
11
       
-
       
    sha256 = "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0";

     

       
9
       
9
       
+
       
    url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2";

     

       
10
       
10
       
+
       
    sha256 = "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m";

     

       
12
       
11
       
 
       
  };

     

       
13
       
12
       
 
       


     

       
13
       
13
       
+
       
  # perl is only used during the check phase.

     

       
14
       
14
       
+
       
  nativeBuildInputs = [ perl ];

     

       
15
       
15
       
+
       


     

       
14
       
16
       
 
       
  buildInputs = [ zlib bzip2 lzma curl ];

     

       
15
       
17
       
 
       


     

       
16
       
18
       
 
       
  configureFlags = "--enable-libcurl"; # optional but strongly recommended

     

       
17
       
19
       
 
       


     

       
18
       
20
       
 
       
  installFlags = "prefix=$(out)";

     

       
19
       
21
       
 
       


     

       
22
       
22
       
+
       
  preCheck = ''

     

       
23
       
23
       
+
       
    patchShebangs test/

     

       
24
       
24
       
+
       
  '';

     

       
25
       
25
       
+
       


     

       
26
       
26
       
+
       
  enableParallelBuilding = true;

     

       
27
       
27
       
+
       


     

       
28
       
28
       
+
       
  doCheck = true;

     

       
29
       
29
       
+
       


     

       
20
       
30
       
 
       
  meta = with stdenv.lib; {

     

       
21
       
31
       
 
       
    description = "A C library for reading/writing high-throughput sequencing data";

     

       
22
       
32
       
 
       
    license = licenses.mit;

     
···

       
25
       
35
       
 
       
    maintainers = [ maintainers.mimadrid ];

     

       
26
       
36
       
 
       
  };

     

       
27
       
37
       
 
       
}

     

       
28
       
28
       
-