From c09e1e540cae359d158bb36137f7c075ad42d71f Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Fri, 19 Sep 2008 13:39:17 +0000
Subject: [PATCH] Introduced pal2nal package

svn path=/nixpkgs/trunk/; revision=12896
---
 .../science/biology/pal2nal/default.nix       | 31 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  4 +++
 2 files changed, 35 insertions(+)
 create mode 100644 pkgs/applications/science/biology/pal2nal/default.nix

diff --git a/pkgs/applications/science/biology/pal2nal/default.nix b/pkgs/applications/science/biology/pal2nal/default.nix
new file mode 100644
index 000000000000..ff9e35d92164
--- /dev/null
+++ b/pkgs/applications/science/biology/pal2nal/default.nix
@@ -0,0 +1,31 @@
+{stdenv, fetchurl, perl, paml}:
+
+stdenv.mkDerivation {
+  name = "pal2nal-12";
+  src = fetchurl {
+    url = http://coot.embl.de/pal2nal/distribution/pal2nal.v12.tar.gz;
+    sha256 = "1qj9sq5skpa7vyccl9gxc5ls85jwiq8j6mr8wvacz4yhyg0afy04";
+  };
+
+  installPhase = ''
+    ensureDir $out/bin
+
+    cp -v pal2nal.pl $out/bin 
+
+    ensureDir $out/doc
+
+    cp -v README $out/doc
+  '';
+
+  meta = {
+    description     = "Program for aligning nucleotide sequences based on an aminoacid alignment";
+    longDescription = ''
+   PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (KS) and non-synonymous (KA) substitution rates.
+
+If the input is a pair of sequences, PAL2NAL automatically calculates KS and KA by the codeml program in PAML.
+'';
+    license        = "non-commercial";
+    homepage       = http://coot.embl.de/pal2nal/;
+    pkgMaintainer  = "Pjotr Prins";
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 34718f2cb245..c53e8a9821d2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -7304,6 +7304,10 @@ let
     inherit fetchurl stdenv;
   };
 
+  pal2nal = import ../applications/science/biology/pal2nal {
+    inherit fetchurl stdenv perl paml;
+  };
+
   ### SCIENCE/LOGIC
 
   coq = import ../applications/science/logic/coq {