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

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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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{ lib, stdenv, fetchurl, hmmer, perl }:
itsx: init at 1.1.1
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stdenv.mkDerivation rec {
version = "1.1.1";
treewide: name -> pname (easy cases) (#66585) treewide replacement of stdenv.mkDerivation rec { name = "*-${version}"; version = "*"; to pname
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pname = "itsx";
itsx: init at 1.1.1
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src = fetchurl {
url = "http://microbiology.se/sw/ITSx_${version}.tar.gz";
sha256 = "0lrmy2n3ax7f208k0k8l3yz0j5cpz05hv4hx1nnxzn0c51z1pc31";
};
buildInputs = [ hmmer perl ];
buildPhase = ''
sed -e "s,profileDB = .*,profileDB = \"$out/share/ITSx_db/HMMs\";," -i ITSx
sed "3 a \$ENV{\'PATH\'}='${hmmer}/bin:'.\"\$ENV{\'PATH\'}\";" -i ITSx
mkdir bin
mv ITSx bin
'';
installPhase = ''
mkdir -p $out/share/doc && cp -a bin $out/
cp *pdf $out/share/doc
cp -r ITSx_db $out/share
'';
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 07:54:33 +00:00
meta = with lib; {
itsx: init at 1.1.1
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description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing";
treewide: Per RFC45, remove all unquoted URLs
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homepage = "https://microbiology.se/software/itsx/";
itsx: init at 1.1.1
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license = licenses.gpl3;
maintainers = [ maintainers.bzizou ];
itsx: enable on darwin
2020-07-28 19:48:55 +01:00
platforms = platforms.unix;
itsx: init at 1.1.1
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};
}
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