diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index b6fc8af4324..db12fc00c87 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -1,22 +1,18 @@ -{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl, bash }: +{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "bcftools"; - major = "1.6"; - version = "${major}.0"; + version = "1.6"; src = fetchurl { - url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2"; + url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2"; sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19"; }; + nativeBuildInputs = [ perl ]; - nativeBuildInputs = [ bash ]; - - buildInputs = [ zlib bzip2 lzma ]; - - propagatedBuildInputs = [ htslib ]; + buildInputs = [ htslib zlib bzip2 lzma curl ]; makeFlags = [ "HSTDIR=${htslib}" @@ -24,15 +20,16 @@ stdenv.mkDerivation rec { "CC=cc" ]; + preCheck = '' + patchShebangs misc/ + patchShebangs test/ + sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl + ''; + enableParallelBuilding = 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; { description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; license = licenses.mit;