nixpkgs/pkgs/applications/science/biology/arb/default.nix

args: with args;

# NOTE: This package does not build on 64-bit systems. Because of some faulty
# int->pointer arithmatic. The build scripts are abnormal - but it appears to
# work.

stdenv.mkDerivation {
  name = "arb-2007-Dec-07";
  src = fetchurl {
    url = http://download.arb-home.de/release/2007_12_07/arbsrc.tgz;
    sha256 = "04l7qj0wigg1h56a9d70hxhdr343v3dg5dhqrc7fahc1v4h8f1rd";
  };

  patches = [ ./makefile.patch ];

  buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];

  unpackPhase = ''
    tar xzf $src
  '';

  buildPhase = ''
    echo `make`   # avoids error signal
    export ARBHOME=`pwd`
    export PATH=$ARBHOME/bin:$PATH
    make all
  '';

  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
    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
    rm -vrf lib/nas
    ln -vs $datadir/lib/nas $out/lib/nas
    # bulk copy
    cp -vau * $out
    # replace arb script
    mv $out/bin/arb $out/bin/arb.orig
    cat > $out/bin/arb << ARB 
#!/bin/sh

echo Starting Nix compiled arb from $out
echo Shared databases are located in $datadir
export ARBHOME=$out
export LD_LIBRARY=$ARBHOME/lib

$out/bin/arb_ntree $*

ARB
    chmod +x $out/bin/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''; 
    license     = "non-free";
    pkgMaintainer = "Pjotr Prins";
    homepage    = http://www.arb-home.de/;
  };
}