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sortmerna: 4.2.0 -> 4.3.7

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emaryn 2025-03-01 12:37:08 +08:00 • committed by emaryn
parent 297523cc07
commit f27d4d4a36
1 changed files with 17 additions and 14 deletions
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31
pkgs/by-name/so/sortmerna/package.nix
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@ -11,22 +11,29 @@
let let
rocksdb = rocksdb_8_3; rocksdb = rocksdb_8_3;
concurrentqueue = fetchFromGitHub {
owner = "cameron314";
repo = "concurrentqueue";
tag = "v1.0.4";
hash = "sha256-MkhlDme6ZwKPuRINhfpv7cxliI2GU3RmTfC6O0ke/IQ=";
};
in in
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "sortmerna"; pname = "sortmerna";
version = "4.2.0"; version = "4.3.7";
src = fetchFromGitHub { src = fetchFromGitHub {
owner = "sortmerna";
repo = "sortmerna"; repo = "sortmerna";
owner = "biocore"; tag = "v${version}";
rev = "v${version}"; hash = "sha256-oxwZBkeW3usEcJE1XLu1UigKsgOsljwGFTpb7U3845I=";
sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
}; };
nativeBuildInputs = [ nativeBuildInputs = [
cmake cmake
pkg-config pkg-config
]; ];
buildInputs = [ buildInputs = [
zlib zlib
rocksdb rocksdb
@ -37,19 +44,15 @@ stdenv.mkDerivation rec {
"-DPORTABLE=off" "-DPORTABLE=off"
"-DRAPIDJSON_HOME=${rapidjson}" "-DRAPIDJSON_HOME=${rapidjson}"
"-DROCKSDB_HOME=${rocksdb}" "-DROCKSDB_HOME=${rocksdb}"
"-DCONCURRENTQUEUE_HOME=${concurrentqueue}"
"-DROCKSDB_STATIC=off" "-DROCKSDB_STATIC=off"
"-DZLIB_STATIC=off" "-DZLIB_STATIC=off"
]; ];
postPatch = '' 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. # Fix missing pthread dependency for the main binary.
substituteInPlace src/sortmerna/CMakeLists.txt \ substituteInPlace src/sortmerna/CMakeLists.txt \
--replace "target_link_libraries(sortmerna" \ --replace-fail "target_link_libraries(sortmerna" \
"target_link_libraries(sortmerna Threads::Threads" "target_link_libraries(sortmerna Threads::Threads"
# Fix gcc-13 build by adding missing <cstdint> includes: # Fix gcc-13 build by adding missing <cstdint> includes:
@ -57,13 +60,13 @@ stdenv.mkDerivation rec {
sed -e '1i #include <cstdint>' -i include/kseq_load.hpp sed -e '1i #include <cstdint>' -i include/kseq_load.hpp
''; '';
meta = with lib; { meta = {
description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
mainProgram = "sortmerna"; mainProgram = "sortmerna";
license = licenses.lgpl3; license = lib.licenses.lgpl3;
platforms = platforms.x86_64; platforms = lib.platforms.x86_64;
homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/"; homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
maintainers = with maintainers; [ luispedro ]; maintainers = with lib.maintainers; [ luispedro ];
broken = stdenv.hostPlatform.isDarwin; broken = stdenv.hostPlatform.isDarwin;
}; };
} }