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{ lib, stdenv, fetchurl, fetchpatch, zlib, htslib, perl, ncurses ? null }:
stdenv.mkDerivation rec {
pname = "samtools";
version = "1.17";
src = fetchurl {
url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
sha256 = "sha256-Ot85C2KCGf1kCPFGAqTEqpDmPhizldrXIqtRlDiipyk";
};
# tests require `bgzip` from the htslib package
nativeCheckInputs = [ htslib ];
nativeBuildInputs = [ perl ];
buildInputs = [ zlib ncurses htslib ];
preConfigure = lib.optional stdenv.hostPlatform.isStatic ''
export LIBS="-lz -lbz2 -llzma"
'';
makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
configureFlags = [ "--with-htslib=${htslib}" ]
++ lib.optional (ncurses == null) "--without-curses"
++ lib.optionals stdenv.hostPlatform.isStatic ["--without-curses" ]
;
preCheck = ''
patchShebangs test/
'';
enableParallelBuilding = true;
doCheck = true;
meta = with lib; {
description = "Tools for manipulating SAM/BAM/CRAM format";
license = licenses.mit;
homepage = "http://www.htslib.org/";
platforms = platforms.unix;
maintainers = with maintainers; [ mimame unode ];
};
}
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