From 9fbf8625f19003c2be1addbe0d9f5c4ecbda9a1d Mon Sep 17 00:00:00 2001
From: Bruno Bzeznik <Bruno.Bzeznik@imag.fr>
Date: Thu, 13 Jun 2019 14:35:13 +0200
Subject: [PATCH] cd-hit: init at 4.8.1

---
 .../science/biology/cd-hit/default.nix        | 34 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 36 insertions(+)
 create mode 100644 pkgs/applications/science/biology/cd-hit/default.nix

diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/applications/science/biology/cd-hit/default.nix
new file mode 100644
index 000000000000..1a41a28a19aa
--- /dev/null
+++ b/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;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 33464ab30a45..1bbec7914fb2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21628,6 +21628,8 @@ in
 
   bftools = callPackage ../applications/science/biology/bftools { };
 
+  cd-hit = callPackage ../applications/science/biology/cd-hit { };
+
   cmtk = callPackage ../applications/science/biology/cmtk { };
 
   conglomerate = callPackage ../applications/science/biology/conglomerate { };