nixpkgs/pkgs/applications/science/biology/sortmerna/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

46 lines
1.3 KiB
Nix

{ lib, stdenv, cmake, rocksdb, rapidjson, pkgconfig, fetchFromGitHub, fetchpatch, zlib }:
stdenv.mkDerivation rec {
pname = "sortmerna";
version = "4.2.0";
src = fetchFromGitHub {
repo = pname;
owner = "biocore";
rev = "v${version}";
sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
};
nativeBuildInputs = [ cmake pkgconfig ];
buildInputs = [ zlib rocksdb rapidjson ];
cmakeFlags = [
"-DCMAKE_BUILD_TYPE=Release"
"-DPORTABLE=off"
"-DRAPIDJSON_HOME=${rapidjson}"
"-DROCKSDB_HOME=${rocksdb}"
"-DROCKSDB_STATIC=off"
"-DZLIB_STATIC=off"
];
postPatch = ''
# Fix formatting string error:
# https://github.com/biocore/sortmerna/issues/255
substituteInPlace src/sortmerna/indexdb.cpp \
--replace 'is_verbose, ss' 'is_verbose, "%s", ss'
# Fix missing pthread dependency for the main binary.
substituteInPlace src/sortmerna/CMakeLists.txt \
--replace "target_link_libraries(sortmerna" \
"target_link_libraries(sortmerna Threads::Threads"
'';
meta = with lib; {
description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
license = licenses.lgpl3;
platforms = platforms.x86_64;
homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
maintainers = with maintainers; [ luispedro ];
};
}