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bcftools: fix up

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This commit is contained in:
Orivej Desh 2017-10-01 07:31:55 +00:00
parent 09a5396982
commit d73bd7f50a
1 changed files with 11 additions and 14 deletions
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25
pkgs/applications/science/biology/bcftools/default.nix
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@ -1,22 +1,18 @@
{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl, bash }: { 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 = "1.6"; 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}/${name}.tar.bz2";
sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19"; sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
}; };
nativeBuildInputs = [ perl ];
nativeBuildInputs = [ bash ]; buildInputs = [ htslib zlib bzip2 lzma curl ];
buildInputs = [ zlib bzip2 lzma ];
propagatedBuildInputs = [ htslib ];
makeFlags = [ makeFlags = [
"HSTDIR=${htslib}" "HSTDIR=${htslib}"
@ -24,15 +20,16 @@ stdenv.mkDerivation rec {
"CC=cc" "CC=cc"
]; ];
preCheck = ''
patchShebangs misc/
patchShebangs test/
sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl
'';
enableParallelBuilding = true; enableParallelBuilding = true;
doCheck = true; doCheck = true;
preCheck = ''
sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl test/csq/{sort-csq,make-csq-test} misc/plot-vcfstats
sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl
'';
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;