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 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+rwx $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+rwx $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 $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. }; }