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Merge pull request #29963 from mimadrid/update/samtools-1.6.0 

samtools: 1.5.0 -> 1.6.0
This commit is contained in:
Orivej Desh 2017-10-02 01:07:11 +00:00 committed by GitHub
parent d2bd006166 d73bd7f50a
commit 047c576353
3 changed files with 47 additions and 18 deletions
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23
pkgs/applications/science/biology/bcftools/default.nix
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@ -1,17 +1,18 @@
{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }: { stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
pname = "bcftools"; pname = "bcftools";
major = "1.5"; version = "1.6";
version = "${major}.0";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2"; url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2";
sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"; sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
}; };
buildInputs = [ zlib bzip2 lzma perl ]; nativeBuildInputs = [ perl ];
buildInputs = [ htslib zlib bzip2 lzma curl ];
makeFlags = [ makeFlags = [
"HSTDIR=${htslib}" "HSTDIR=${htslib}"
@ -19,6 +20,16 @@ stdenv.mkDerivation rec {
"CC=cc" "CC=cc"
]; ];
preCheck = ''
patchShebangs misc/
patchShebangs test/
sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl
'';
enableParallelBuilding = true;
doCheck = true;
meta = with stdenv.lib; { meta = with stdenv.lib; {
description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";
license = licenses.mit; license = licenses.mit;

21
pkgs/applications/science/biology/samtools/default.nix
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@ -1,21 +1,30 @@
{ stdenv, fetchurl, zlib, htslib, ncurses ? null }: { stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
pname = "samtools"; pname = "samtools";
major = "1.5"; version = "1.6";
version = "${major}.0";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2"; url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"; sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f";
}; };
buildInputs = [ zlib ncurses ]; nativeBuildInputs = [ perl ];
buildInputs = [ zlib ncurses htslib ];
configureFlags = [ "--with-htslib=${htslib}" ] configureFlags = [ "--with-htslib=${htslib}" ]
++ stdenv.lib.optional (ncurses == null) "--without-curses"; ++ stdenv.lib.optional (ncurses == null) "--without-curses";
preCheck = ''
patchShebangs test/
'';
enableParallelBuilding = true;
doCheck = true;
meta = with stdenv.lib; { meta = with stdenv.lib; {
description = "Tools for manipulating SAM/BAM/CRAM format"; description = "Tools for manipulating SAM/BAM/CRAM format";
license = licenses.mit; license = licenses.mit;

21
pkgs/development/libraries/science/biology/htslib/default.nix
View File

@ -1,22 +1,32 @@
{ stdenv, fetchurl, zlib, bzip2, lzma, curl }: { stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
version = "${major}.0";
pname = "htslib"; pname = "htslib";
major = "1.5"; version = "1.6";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2"; url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2";
sha256 = "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0"; sha256 = "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m";
}; };
# perl is only used during the check phase.
nativeBuildInputs = [ perl ];
buildInputs = [ zlib bzip2 lzma curl ]; buildInputs = [ zlib bzip2 lzma curl ];
configureFlags = "--enable-libcurl"; # optional but strongly recommended configureFlags = "--enable-libcurl"; # optional but strongly recommended
installFlags = "prefix=$(out)"; installFlags = "prefix=$(out)";
preCheck = ''
patchShebangs test/
'';
enableParallelBuilding = true;
doCheck = true;
meta = with stdenv.lib; { meta = with stdenv.lib; {
description = "A C library for reading/writing high-throughput sequencing data"; description = "A C library for reading/writing high-throughput sequencing data";
license = licenses.mit; license = licenses.mit;
@ -25,4 +35,3 @@ stdenv.mkDerivation rec {
maintainers = [ maintainers.mimadrid ]; maintainers = [ maintainers.mimadrid ];
}; };
} }