nixpkgs/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix

{ lib, stdenv, fetchurl, zlib }:

stdenv.mkDerivation rec {
  pname = "samtools";
  version = "0.1.19";

  src = fetchurl {
    url = "mirror://sourceforge/samtools/${pname}-${version}.tar.bz2";
    sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4";
  };

  patches = [
    ./samtools-0.1.19-no-curses.patch
  ];

  buildInputs = [ zlib ];

  installPhase = ''
    mkdir -p $out/bin
    mkdir -p $out/share/man

    cp samtools $out/bin
    cp samtools.1 $out/share/man
  '';

  meta = with lib; {
    description = "Tools for manipulating SAM/BAM/CRAM format";
    license = licenses.mit;
    homepage = "http://samtools.sourceforge.net/";
    platforms = platforms.unix;
    maintainers = [ maintainers.unode ];
  };
}
treewide: with stdenv.lib; in meta -> with lib; Part of: https://github.com/NixOS/nixpkgs/issues/108938 meta = with stdenv.lib; is a widely used pattern. We want to slowly remove the `stdenv.lib` indirection and encourage people to use `lib` directly. Thus let’s start with the meta field. This used a rewriting script to mostly automatically replace all occurances of this pattern, and add the `lib` argument to the package header if it doesn’t exist yet. The script in its current form is available at https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix 2021-01-11 07:54:33 +00:00			`{ lib, stdenv, fetchurl, zlib }:`
samtools_0_1_19: init at 0.1.19 samtools-1.5 already exists but some software requires the older version 2018-02-02 01:51:34 +00:00
			`stdenv.mkDerivation rec {`
			`pname = "samtools";`
			`version = "0.1.19";`

			`src = fetchurl {`
treewide: name -> pname (easy cases) (#66585) treewide replacement of stdenv.mkDerivation rec { name = "-${version}"; version = ""; to pname 2019-08-15 13:41:18 +01:00			`url = "mirror://sourceforge/samtools/${pname}-${version}.tar.bz2";`
samtools_0_1_19: init at 0.1.19 samtools-1.5 already exists but some software requires the older version 2018-02-02 01:51:34 +00:00			`sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4";`
			`};`

			`patches = [`
			`./samtools-0.1.19-no-curses.patch`
			`];`

			`buildInputs = [ zlib ];`

			`installPhase = ''`
			`mkdir -p $out/bin`
			`mkdir -p $out/share/man`

			`cp samtools $out/bin`
			`cp samtools.1 $out/share/man`
			`'';`

treewide: with stdenv.lib; in meta -> with lib; Part of: https://github.com/NixOS/nixpkgs/issues/108938 meta = with stdenv.lib; is a widely used pattern. We want to slowly remove the `stdenv.lib` indirection and encourage people to use `lib` directly. Thus let’s start with the meta field. This used a rewriting script to mostly automatically replace all occurances of this pattern, and add the `lib` argument to the package header if it doesn’t exist yet. The script in its current form is available at https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix 2021-01-11 07:54:33 +00:00			`meta = with lib; {`
samtools_0_1_19: init at 0.1.19 samtools-1.5 already exists but some software requires the older version 2018-02-02 01:51:34 +00:00			`description = "Tools for manipulating SAM/BAM/CRAM format";`
			`license = licenses.mit;`
treewide: Per RFC45, remove all unquoted URLs 2020-04-01 02:11:51 +01:00			`homepage = "http://samtools.sourceforge.net/";`
samtools_0_1_19: init at 0.1.19 samtools-1.5 already exists but some software requires the older version 2018-02-02 01:51:34 +00:00			`platforms = platforms.unix;`
			`maintainers = [ maintainers.unode ];`
			`};`
			`}`