public
/
nixpkgs
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added shared dir and updated reference to ARB 

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
pkgs/applications/science/biology/arb/default.nix
View File

@ -27,19 +27,26 @@ stdenv.mkDerivation {
''; '';
installPhase = '' installPhase = ''
datadir=/nix/var/lib/arb
ensureDir $out/lib ensureDir $out/lib
# link out shared location shareddir=/nix/var/lib/arb
ensureDir $datadir/lib/pts # link out writable shared location lib/pts
chmod a+rwx $datadir/lib/pts ensureDir $shareddir/lib/pts
# cp -vau lib/pts $datadir/lib cp -vau lib/pts $shareddir/lib
rm -vrf lib/pts rm -vrf lib/pts
ln -vs $datadir/lib/pts $out/lib/pts ln -vs $shareddir/lib/pts $out/lib/pts
# link out shared location chmod a+rw -R $shareddir/lib/pts
ensureDir $datadir/lib/nas # link out writable shared location lib/nas/
cp -vau lib/nas $datadir/lib ensureDir $shareddir/lib/nas
cp -vau lib/nas $shareddir/lib
rm -vrf lib/nas 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 # bulk copy
cp -vau * $out cp -vau * $out
# replace arb script # replace arb script
@ -48,9 +55,10 @@ stdenv.mkDerivation {
#!/bin/sh #!/bin/sh
echo Starting Nix compiled arb from $out 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 ARBHOME=$out
export LD_LIBRARY=$ARBHOME/lib export LD_LIBRARY=$ARBHOME/lib
$out/bin/arb_ntree $* $out/bin/arb_ntree $*
@ -60,9 +68,10 @@ ARB
meta = { meta = {
description = "ARB software for sequence database handling and analysis"; 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"; license = "non-free";
pkgMaintainer = "Pjotr Prins"; pkgMaintainer = "http://BioLib.open-bio.org/";
homepage = http://www.arb-home.de/; homepage = http://www.arb-home.de/;
priority = "10"; # because it includes binaries of clustal etc.
}; };
} }