109 lines
3.5 KiB
Nix
109 lines
3.5 KiB
Nix
{ lib, stdenv, buildPackages, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }:
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stdenv.mkDerivation rec {
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pname = "blast";
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version = "2.11.0";
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src = fetchurl {
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url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz";
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sha256 = "0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq";
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};
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sourceRoot = "ncbi-blast-${version}+-src/c++";
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configureFlags = [
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# With flat Makefile we can use all_projects in order not to build extra.
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# These extra cause clang to hang on Darwin.
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"--with-flat-makefile"
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"--without-makefile-auto-update"
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"--with-dll" # build dynamic libraries (static are default)
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];
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makeFlags = [ "all_projects=app/" ];
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preConfigure = ''
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export NCBICXX_RECONF_POLICY=warn
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export PWD=$(pwd)
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export HOME=$PWD
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# The configure scripts wants to set AR="ar cr" unless it is already set in
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# the environment. Because stdenv sets AR="ar", the result is a bad call to
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# the assembler later in the process. Thus, we need to unset AR
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unset AR
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for awks in scripts/common/impl/is_log_interesting.awk \
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scripts/common/impl/report_duplicates.awk; do
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substituteInPlace $awks \
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--replace /usr/bin/awk ${gawk}/bin/awk
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done
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for mk in src/build-system/Makefile.meta.in \
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src/build-system/helpers/run_with_lock.c ; do
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substituteInPlace $mk \
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--replace /bin/rm ${coreutils}/bin/rm
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done
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for mk in src/build-system/Makefile.meta.gmake=no \
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src/build-system/Makefile.meta_l \
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src/build-system/Makefile.meta_r \
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src/build-system/Makefile.requirements \
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src/build-system/Makefile.rules_with_autodep.in; do
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substituteInPlace $mk \
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--replace /bin/echo ${coreutils}/bin/echo
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done
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for mk in src/build-system/Makefile.meta_p \
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src/build-system/Makefile.rules_with_autodep.in \
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src/build-system/Makefile.protobuf.in ; do
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substituteInPlace $mk \
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--replace /bin/mv ${coreutils}/bin/mv
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done
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substituteInPlace src/build-system/configure \
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--replace /bin/pwd ${coreutils}/bin/pwd \
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--replace /bin/ln ${coreutils}/bin/ln
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substituteInPlace src/build-system/configure.ac \
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--replace /bin/pwd ${coreutils}/bin/pwd \
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--replace /bin/ln ${coreutils}/bin/ln
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substituteInPlace src/build-system/Makefile.meta_l \
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--replace /bin/date ${coreutils}/bin/date
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'';
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depsBuildBuild = [ buildPackages.stdenv.cc ];
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nativeBuildInputs = [ perl ];
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# perl is necessary in buildInputs so that installed perl scripts get patched
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# correctly
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buildInputs = [ coreutils perl gawk zlib bzip2 cpio ]
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++ lib.optionals stdenv.isDarwin [ ApplicationServices ];
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hardeningDisable = [ "format" ];
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postInstall = ''
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substituteInPlace $out/bin/get_species_taxids.sh \
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--replace /bin/rm ${coreutils}/bin/rm
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'';
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patches = [ ./no_slash_bin.patch ];
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enableParallelBuilding = true;
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# Many tests require either network access or locally available databases
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doCheck = false;
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meta = with lib; {
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description = ''Basic Local Alignment Search Tool (BLAST) finds regions of
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similarity between biological sequences'';
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homepage = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
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license = licenses.publicDomain;
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# Version 2.10.0 fails on Darwin
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# See https://github.com/NixOS/nixpkgs/pull/61430
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platforms = platforms.linux;
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maintainers = with maintainers; [ luispedro ];
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};
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}
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