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nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix

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treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix continuation of #109595 pkgconfig was aliased in 2018, however, it remained in all-packages.nix due to its wide usage. This cleans up the remaining references to pkgs.pkgsconfig and moves the entry to aliases.nix. python3Packages.pkgconfig remained unchanged because it's the canonical name of the upstream package on pypi.
2021-01-19 06:50:56 +00:00
{ lib, stdenv, cmake, rocksdb, rapidjson, pkg-config, fetchFromGitHub, fetchpatch, zlib }:
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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stdenv.mkDerivation rec {
pname = "sortmerna";
sortmerna: 3.0.3 -> 4.2.0 - Fixes build against rocksdb 6.10.2 - Use dynamic rocksdb and zlib libraries - Build a dynamic binary
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version = "4.2.0";
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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src = fetchFromGitHub {
repo = pname;
owner = "biocore";
rev = "v${version}";
sortmerna: 3.0.3 -> 4.2.0 - Fixes build against rocksdb 6.10.2 - Use dynamic rocksdb and zlib libraries - Build a dynamic binary
2020-07-18 14:14:20 +01:00
sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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};
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix continuation of #109595 pkgconfig was aliased in 2018, however, it remained in all-packages.nix due to its wide usage. This cleans up the remaining references to pkgs.pkgsconfig and moves the entry to aliases.nix. python3Packages.pkgconfig remained unchanged because it's the canonical name of the upstream package on pypi.
2021-01-19 06:50:56 +00:00
nativeBuildInputs = [ cmake pkg-config ];
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
2019-07-12 14:35:03 +01:00
buildInputs = [ zlib rocksdb rapidjson ];
cmakeFlags = [
"-DCMAKE_BUILD_TYPE=Release"
sortmerna: 3.0.3 -> 4.2.0 - Fixes build against rocksdb 6.10.2 - Use dynamic rocksdb and zlib libraries - Build a dynamic binary
2020-07-18 14:14:20 +01:00
"-DPORTABLE=off"
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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"-DRAPIDJSON_HOME=${rapidjson}"
sortmerna: 3.0.3 -> 4.2.0 - Fixes build against rocksdb 6.10.2 - Use dynamic rocksdb and zlib libraries - Build a dynamic binary
2020-07-18 14:14:20 +01:00
"-DROCKSDB_HOME=${rocksdb}"
"-DROCKSDB_STATIC=off"
"-DZLIB_STATIC=off"
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
2019-07-12 14:35:03 +01:00
];
sortmerna: 3.0.3 -> 4.2.0 - Fixes build against rocksdb 6.10.2 - Use dynamic rocksdb and zlib libraries - Build a dynamic binary
2020-07-18 14:14:20 +01:00
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"
'';
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
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meta = with lib; {
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
license = licenses.lgpl3;
platforms = platforms.x86_64;
treewide: Per RFC45, remove all unquoted URLs
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homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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maintainers = with maintainers; [ luispedro ];
sortmerna: mark broken on darwin
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broken = stdenv.isDarwin;
sortmerna: init at 3.0.3 This is a useful package in bioinformatics, namely in processing short-read sequencing data from metagenomes
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};
}
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