{ lib, stdenv, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }: stdenv.mkDerivation rec { pname = "blast"; version = "2.10.0"; src = fetchurl { url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz"; sha256 = "09nry5knj5hhxpn0a5ww1gb1704grd4r1y7adbjl6kqwq37dkk9s"; }; sourceRoot = "ncbi-blast-${version}+-src/c++"; configureFlags = [ # With flat Makefile we can use all_projects in order not to build extra. # These extra cause clang to hang on Darwin. "--with-flat-makefile" "--without-makefile-auto-update" "--with-dll" # build dynamic libraries (static are default) ]; makeFlags = [ "all_projects=app/" ]; preConfigure = '' export NCBICXX_RECONF_POLICY=warn export PWD=$(pwd) export HOME=$PWD # The configure scripts wants to set AR="ar cr" unless it is already set in # the environment. Because stdenv sets AR="ar", the result is a bad call to # the assembler later in the process. Thus, we need to unset AR unset AR for awks in scripts/common/impl/is_log_interesting.awk \ scripts/common/impl/report_duplicates.awk; do substituteInPlace $awks \ --replace /usr/bin/awk ${gawk}/bin/awk done for mk in src/build-system/Makefile.meta.in \ src/build-system/helpers/run_with_lock.c ; do substituteInPlace $mk \ --replace /bin/rm ${coreutils}/bin/rm done for mk in src/build-system/Makefile.meta.gmake=no \ src/build-system/Makefile.meta_l \ src/build-system/Makefile.meta_r \ src/build-system/Makefile.requirements \ src/build-system/Makefile.rules_with_autodep.in; do substituteInPlace $mk \ --replace /bin/echo ${coreutils}/bin/echo done for mk in src/build-system/Makefile.meta_p \ src/build-system/Makefile.rules_with_autodep.in \ src/build-system/Makefile.protobuf.in ; do substituteInPlace $mk \ --replace /bin/mv ${coreutils}/bin/mv done substituteInPlace src/build-system/configure \ --replace /bin/pwd ${coreutils}/bin/pwd \ --replace /bin/ln ${coreutils}/bin/ln substituteInPlace src/build-system/configure.ac \ --replace /bin/pwd ${coreutils}/bin/pwd \ --replace /bin/ln ${coreutils}/bin/ln substituteInPlace src/build-system/Makefile.meta_l \ --replace /bin/date ${coreutils}/bin/date ''; nativeBuildInputs = [ perl ]; # perl is necessary in buildInputs so that installed perl scripts get patched # correctly buildInputs = [ coreutils perl gawk zlib bzip2 cpio ] ++ lib.optionals stdenv.isDarwin [ ApplicationServices ]; hardeningDisable = [ "format" ]; postInstall = '' substituteInPlace $out/bin/get_species_taxids.sh \ --replace /bin/rm ${coreutils}/bin/rm ''; patches = [ ./no_slash_bin.patch ]; enableParallelBuilding = true; # Many tests require either network access or locally available databases doCheck = false; meta = with lib; { description = ''Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences''; homepage = "https://blast.ncbi.nlm.nih.gov/Blast.cgi"; license = licenses.publicDomain; # Version 2.10.0 fails on Darwin # See https://github.com/NixOS/nixpkgs/pull/61430 platforms = platforms.linux; maintainers = with maintainers; [ luispedro ]; }; }