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Small fixes to ARB

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Included older kernel headers

svn path=/nixpkgs/trunk/; revision=12961
This commit is contained in:
Pjotr Prins 2008-10-05 10:56:47 +00:00
parent 512b18ea4a
commit 6d70506401
2 changed files with 17 additions and 33 deletions
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39
pkgs/applications/science/biology/arb/default.nix
View file

@ -13,7 +13,7 @@ stdenv.mkDerivation {
patches = [ ./makefile.patch ];
buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];
unpackPhase = ''
tar xzf $src
@ -27,26 +27,19 @@ stdenv.mkDerivation {
'';
installPhase = ''
datadir=/nix/var/lib/arb
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
# 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 $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
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 $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
ln -vs $datadir/lib/nas $out/lib/nas
# bulk copy
cp -vau * $out
# replace arb script
@ -55,10 +48,9 @@ stdenv.mkDerivation {
#!/bin/sh
echo Starting Nix compiled arb from $out
echo Shared databases are located in $shareddir
# sometimes local profiles override these:
echo Shared databases are located in $datadir
export ARBHOME=$out
export LD_LIBRARY=$ARBHOME/lib
export LD_LIBRARY=$ARBHOME/lib
$out/bin/arb_ntree $*
@ -68,10 +60,9 @@ 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.'';
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 = "http://BioLib.open-bio.org/";
pkgMaintainer = "Pjotr Prins";
homepage = http://www.arb-home.de/;
priority = "10"; # because it includes binaries of clustal etc.
};
}

11
pkgs/top-level/all-packages.nix
View file

@ -4979,11 +4979,6 @@ let
kernelHeaders = kernelHeaders_2_6_23;
kernelHeaders_2_6_18 = import ../os-specific/linux/kernel-headers/2.6.18.5.nix {
inherit fetchurl stdenv unifdef;
};
kernelHeaders_2_6_21 = import ../os-specific/linux/kernel-headers/2.6.21.3.nix {
inherit fetchurl stdenv;
};
@ -7345,11 +7340,9 @@ let
arb = import ../applications/science/biology/arb {
inherit fetchurl stdenv readline libpng zlib x11 lesstif freeglut perl;
inherit (xlibs) libXpm libXaw libX11 libXext libXt;
inherit (xlibs) libXpm libXaw;
# motif = lesstif;
inherit mesa glew libtiff lynx rxp sablotron jdk transfig;
# supporting tools
inherit gv xfig gnuplot;
inherit mesa glew libtiff lynx rxp sablotron jdk;
};
biolib = import ../development/libraries/science/biology/biolib {