78 lines
2.6 KiB
Nix
78 lines
2.6 KiB
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 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
|
|
|
|
unpackPhase = ''
|
|
tar xzf $src
|
|
'';
|
|
|
|
buildPhase = ''
|
|
echo `make` # avoids error signal
|
|
export ARBHOME=`pwd`
|
|
export PATH=$ARBHOME/bin:$PATH
|
|
make all
|
|
'';
|
|
|
|
installPhase = ''
|
|
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
|
|
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
|
|
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
|
|
# 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 $shareddir
|
|
# sometimes local profiles override these:
|
|
export ARBHOME=$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. Note that this package includes its own older versions of clustal etc.'';
|
|
license = "non-free";
|
|
pkgMaintainer = "http://BioLib.open-bio.org/";
|
|
homepage = http://www.arb-home.de/;
|
|
priority = "10"; # because it includes binaries of clustal etc.
|
|
};
|
|
}
|