From 6d70506401f1d3c598ae031ca0b622cf03c5097f Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Sun, 5 Oct 2008 10:56:47 +0000
Subject: Small fixes to ARB Included older kernel headers

svn path=/nixpkgs/trunk/; revision=12961
---
 pkgs/applications/science/biology/arb/default.nix | 39 +++++++++--------------
 1 file changed, 15 insertions(+), 24 deletions(-)

(limited to 'pkgs/applications/science/biology')

diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix
index 5043462b81f2..d84d4f081c66 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 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
+  buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];
 
   unpackPhase = ''
     tar xzf $src
@@ -27,26 +27,19 @@ stdenv.mkDerivation {
   '';
 
   installPhase = ''
+    datadir=/nix/var/lib/arb
     ensureDir $out/lib
-    shareddir=/nix/var/lib/arb
-    # link out writable shared location lib/pts
-    ensureDir $shareddir/lib/pts
-    cp -vau lib/pts $shareddir/lib
+    # link out shared location
+    ensureDir $datadir/lib/pts
+    chmod a+rwx $datadir/lib/pts
+    # cp -vau lib/pts $datadir/lib
     rm -vrf lib/pts
-    ln -vs $shareddir/lib/pts $out/lib/pts
-    chmod a+rw -R $shareddir/lib/pts
-    # link out writable shared location lib/nas/
-    ensureDir $shareddir/lib/nas
-    cp -vau lib/nas $shareddir/lib
+    ln -vs $datadir/lib/pts $out/lib/pts
+    # link out shared location
+    ensureDir $datadir/lib/nas
+    cp -vau lib/nas $datadir/lib
     rm -vrf lib/nas
-    ln -vs $shareddir/lib/nas $out/lib/nas
-    chmod a+rw -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+rw -R $shareddir/lib/pixmaps
+    ln -vs $datadir/lib/nas $out/lib/nas
     # bulk copy
     cp -vau * $out
     # replace arb script
@@ -55,10 +48,9 @@ stdenv.mkDerivation {
 #!/bin/sh
 
 echo Starting Nix compiled arb from $out
-echo Shared databases are located in $shareddir
-# sometimes local profiles override these:
+echo Shared databases are located in $datadir
 export ARBHOME=$out
-export LD_LIBRARY=$ARBHOME/lib   
+export LD_LIBRARY=$ARBHOME/lib
 
 $out/bin/arb_ntree $*
 
@@ -68,10 +60,9 @@ 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. Note that this package includes its own older versions of clustal etc.''; 
+    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''; 
     license     = "non-free";
-    pkgMaintainer = "http://BioLib.open-bio.org/";
+    pkgMaintainer = "Pjotr Prins";
     homepage    = http://www.arb-home.de/;
-    priority    = "10";   # because it includes binaries of clustal etc.
   };
 }
-- 
cgit 1.4.1