Merge pull request #58362 from bzizou/cd-hit

cd-hit: init at 4.8.1

pkgs/applications/science/biology/cd-hit/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+
+stdenv.mkDerivation rec {
+  version = "4.8.1";
+  pname = "cd-hit";
+
+  src = fetchFromGitHub {
+    owner = "weizhongli";
+    repo = "cdhit";
+    rev = "V${version}";
+    sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i";
+  };
+
+  propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick perlPackages.Storable ];
+
+  nativeBuildInputs = [ zlib makeWrapper ];
+
+  makeFlags = [ "PREFIX=$(out)/bin" ];
+
+  preInstall = "mkdir -p $out/bin";
+
+  postFixup = ''
+    wrapProgram $out/bin/FET.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/plot_2d.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/clstr_list_sort.pl --prefix PERL5LIB : $PERL5LIB
+  '';
+  meta = with stdenv.lib; {
+    description = "Clustering and comparing protein or nucleotide sequences";
+    homepage = http://weizhongli-lab.org/cd-hit/;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -22302,6 +22302,8 @@ in
 
   bftools = callPackage ../applications/science/biology/bftools { };
 
+  cd-hit = callPackage ../applications/science/biology/cd-hit { };
+
   cmtk = callPackage ../applications/science/biology/cmtk { };
 
   clustal-omega = callPackage ../applications/science/biology/clustal-omega { };

pkgs/top-level/perl-packages.nix

@@ -16818,6 +16818,19 @@ let
     };
   };
 
+  TextNSP = buildPerlPackage rec {
+    name = "Text-NSP-1.31";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/T/TP/TPEDERSE/${name}.tar.gz";
+      sha256 = "a01201beb29636b3e41ecda2a6cf6522fd265416bd6d994fad02f59fb49cf595";
+    };
+    meta = {
+      description = "Extract collocations and Ngrams from text";
+      license = stdenv.lib.licenses.free;
+      maintainers = [ maintainers.bzizou ];
+    };
+  };
+
   TextvFileasData = buildPerlPackage rec {
     name = "Text-vFile-asData-0.08";
     src = fetchurl {