53 lines
1.5 KiB
Nix
53 lines
1.5 KiB
Nix
{ lib, stdenv, fetchurl, fetchpatch, zlib, htslib, perl, ncurses ? null }:
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stdenv.mkDerivation rec {
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pname = "samtools";
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version = "1.13";
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src = fetchurl {
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url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
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sha256 = "sha256-YWyi4FHMgAmh6cAc/Yx8r4twkW3f9m87dpFAeUZfjGA=";
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};
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patches = [
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# Pull upstream patch for ncurses-6.3 support
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(fetchpatch {
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name = "ncurses-6.3.patch";
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url = "https://github.com/samtools/samtools/commit/396ef20eb0854d6b223c3223b60bb7efe42301f7.patch";
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sha256 = "sha256-p0l9ymXK9nqL2w8EytbW+qeaI7dD86IQgIVxacBj838=";
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})
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];
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# tests require `bgzip` from the htslib package
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checkInputs = [ htslib ];
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nativeBuildInputs = [ perl ];
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buildInputs = [ zlib ncurses htslib ];
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preConfigure = lib.optional stdenv.hostPlatform.isStatic ''
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export LIBS="-lz -lbz2 -llzma"
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'';
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makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
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configureFlags = [ "--with-htslib=${htslib}" ]
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++ lib.optional (ncurses == null) "--without-curses"
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++ lib.optionals stdenv.hostPlatform.isStatic ["--without-curses" ]
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;
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preCheck = ''
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patchShebangs test/
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'';
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enableParallelBuilding = true;
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doCheck = true;
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meta = with lib; {
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description = "Tools for manipulating SAM/BAM/CRAM format";
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license = licenses.mit;
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homepage = "http://www.htslib.org/";
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platforms = platforms.unix;
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maintainers = with maintainers; [ mimame unode ];
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};
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}
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