nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
Profpatsch 4a7f99d55d 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 10:38:22 +01:00

47 lines
1.1 KiB
Nix

{lib, stdenv, fetchFromGitHub, unzip, which, python3, perl}:
stdenv.mkDerivation rec {
pname = "hisat2";
version = "2.2.1";
src = fetchFromGitHub {
owner = "DaehwanKimLab";
repo = "hisat2";
rev = "v${version}";
sha256 = "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754";
};
nativeBuildInputs = [ unzip which ];
buildInputs = [ python3 perl ];
installPhase = ''
mkdir -p $out/bin
cp hisat2 \
hisat2-inspect-l \
hisat2-build-s \
hisat2-align-l \
hisat2-inspect \
hisat2-align-s \
hisat2-inspect-s \
hisat2-build-l \
hisat2-build \
extract_exons.py \
extract_splice_sites.py \
hisat2_extract_exons.py \
hisat2_extract_snps_haplotypes_UCSC.py \
hisat2_extract_snps_haplotypes_VCF.py \
hisat2_extract_splice_sites.py \
hisat2_simulate_reads.py \
$out/bin
'';
meta = with lib; {
description = "Graph based aligner";
license = licenses.gpl3;
homepage = "https://ccb.jhu.edu/software/hisat2/index.shtml";
maintainers = with maintainers; [ jbedo ];
platforms = [ "x86_64-linux" "i686-linux" ];
};
}