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Added shared dir and updated reference to ARB

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svn path=/nixpkgs/trunk/; revision=12958
This commit is contained in:
Pjotr Prins 2008-10-05 10:56:23 +00:00
parent 10e0a6cf6d
commit fcb2efbc92
1 changed files with 23 additions and 14 deletions
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37
pkgs/applications/science/biology/arb/default.nix
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@ -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+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 $datadir/lib/nas $out/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
@ -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.
};
}