From f9e018c80d10f295b16c669decb4e7fec53b0a90 Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Fri, 6 Jun 2008 08:23:49 +0000
Subject: [PATCH] biology/paml added

svn path=/nixpkgs/trunk/; revision=11997
---
 .../science/biology/paml/default.nix          | 32 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  4 +++
 2 files changed, 36 insertions(+)
 create mode 100644 pkgs/applications/science/biology/paml/default.nix

diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix
new file mode 100644
index 000000000000..8e900d7ad3d8
--- /dev/null
+++ b/pkgs/applications/science/biology/paml/default.nix
@@ -0,0 +1,32 @@
+{stdenv, fetchurl}:
+
+stdenv.mkDerivation {
+  name = "paml";
+  src = fetchurl {
+    url = http://abacus.gene.ucl.ac.uk/software/paml4b.tar.gz;
+    sha256 = "0jm9smbkwycwchv6a98yh5xmfw7167p59zpzi5sjz0ka4y7vp3ib";
+  };
+
+  preBuild = ''
+    cd ./src/
+  '';
+  installPhase = ''
+    mkdir -pv $out/bin
+    cp -v codeml $out/bin 
+    cp -v baseml $out/bin
+    cp -v basemlg $out/bin
+    cp -v chi2 $out/bin
+    cp -v codeml $out/bin
+    cp -v evolver $out/bin
+    cp -v mcmctree $out/bin
+    cp -v pamp $out/bin
+    cp -v yn00 $out/bin
+  '';
+
+  meta = {
+    description     = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
+    longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.'';
+    license     = "non-commercial";
+    homepage    = http://abacus.gene.ucl.ac.uk/software/paml.html; 
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index dbe03299b7c2..142648d95ec3 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -6813,6 +6813,10 @@ let pkgs = rec {
     inherit fetchurl stdenv readline;
   };
 
+  paml = import ../applications/science/biology/paml {
+    inherit fetchurl stdenv;
+  };
+
   ### SCIENCE/LOGIC
 
   coq = import ../applications/science/logic/coq {