From bd0b84b3c7362c277021cb7f97b13bce14af5878 Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Mon, 6 Oct 2008 13:17:56 +0000
Subject: [PATCH] Changed arb permissions and priority

svn path=/nixpkgs/trunk/; revision=12969
---
 .../science/biology/arb/default.nix           | 39 ++++++++++++-------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix
index d84d4f081c66..d0feae803937 100644
--- a/pkgs/applications/science/biology/arb/default.nix
+++ b/pkgs/applications/science/biology/arb/default.nix
@@ -13,7 +13,7 @@ stdenv.mkDerivation {
 
   patches = [ ./makefile.patch ];
 
-  buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];
+  buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
 
   unpackPhase = ''
     tar xzf $src
@@ -27,19 +27,26 @@ stdenv.mkDerivation {
   '';
 
   installPhase = ''
-    datadir=/nix/var/lib/arb
     ensureDir $out/lib
-    # link out shared location
-    ensureDir $datadir/lib/pts
-    chmod a+rwx $datadir/lib/pts
-    # cp -vau lib/pts $datadir/lib
+    shareddir=/nix/var/lib/arb
+    # link out writable shared location lib/pts
+    ensureDir $shareddir/lib/pts
+    cp -vau lib/pts $shareddir/lib
     rm -vrf lib/pts
-    ln -vs $datadir/lib/pts $out/lib/pts
-    # link out shared location
-    ensureDir $datadir/lib/nas
-    cp -vau lib/nas $datadir/lib
+    ln -vs $shareddir/lib/pts $out/lib/pts
+    chmod a+rwx -R $shareddir/lib/pts
+    # link out writable shared location lib/nas/
+    ensureDir $shareddir/lib/nas
+    cp -vau lib/nas $shareddir/lib
     rm -vrf lib/nas
-    ln -vs $datadir/lib/nas $out/lib/nas
+    ln -vs $shareddir/lib/nas $out/lib/nas
+    chmod a+rwx -R $shareddir/lib/nas
+    # link out shared lib/pixmaps (not sure about this, yet):
+    ensureDir $shareddir/lib/pixmaps
+    cp -vau lib/pixmaps $shareddir/lib
+    rm -vrf lib/pixmaps
+    ln -vs $shareddir/lib/pixmaps $out/lib/pixmaps
+    chmod a+rwx -R $shareddir/lib/pixmaps
     # bulk copy
     cp -vau * $out
     # replace arb script
@@ -48,9 +55,10 @@ stdenv.mkDerivation {
 #!/bin/sh
 
 echo Starting Nix compiled arb from $out
-echo Shared databases are located in $datadir
+echo Shared databases are located in $shareddir
+# sometimes local profiles override these:
 export ARBHOME=$out
-export LD_LIBRARY=$ARBHOME/lib
+export LD_LIBRARY=$ARBHOME/lib   
 
 $out/bin/arb_ntree $*
 
@@ -60,9 +68,10 @@ ARB
 
   meta = {
     description     = "ARB software for sequence database handling and analysis";
-    longDescription = ''The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria''; 
+    longDescription = ''The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. Note that this package includes its own older versions of clustal etc.''; 
     license     = "non-free";
-    pkgMaintainer = "Pjotr Prins";
+    pkgMaintainer = "http://BioLib.open-bio.org/";
     homepage    = http://www.arb-home.de/;
+    priority    = "10";   # because it includes binaries of clustal etc.
   };
 }