Changed arb permissions and priority
svn path=/nixpkgs/trunk/; revision=12969
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9fdecb1296
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@ -13,7 +13,7 @@ stdenv.mkDerivation {
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patches = [ ./makefile.patch ];
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patches = [ ./makefile.patch ];
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buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];
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buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
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unpackPhase = ''
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unpackPhase = ''
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tar xzf $src
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tar xzf $src
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@ -27,19 +27,26 @@ stdenv.mkDerivation {
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'';
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'';
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installPhase = ''
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installPhase = ''
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datadir=/nix/var/lib/arb
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ensureDir $out/lib
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ensureDir $out/lib
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# link out shared location
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shareddir=/nix/var/lib/arb
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ensureDir $datadir/lib/pts
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# link out writable shared location lib/pts
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chmod a+rwx $datadir/lib/pts
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ensureDir $shareddir/lib/pts
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# cp -vau lib/pts $datadir/lib
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cp -vau lib/pts $shareddir/lib
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rm -vrf lib/pts
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rm -vrf lib/pts
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ln -vs $datadir/lib/pts $out/lib/pts
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ln -vs $shareddir/lib/pts $out/lib/pts
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# link out shared location
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chmod a+rwx -R $shareddir/lib/pts
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ensureDir $datadir/lib/nas
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# link out writable shared location lib/nas/
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cp -vau lib/nas $datadir/lib
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ensureDir $shareddir/lib/nas
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cp -vau lib/nas $shareddir/lib
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rm -vrf lib/nas
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rm -vrf lib/nas
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ln -vs $datadir/lib/nas $out/lib/nas
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ln -vs $shareddir/lib/nas $out/lib/nas
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chmod a+rwx -R $shareddir/lib/nas
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# link out shared lib/pixmaps (not sure about this, yet):
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ensureDir $shareddir/lib/pixmaps
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cp -vau lib/pixmaps $shareddir/lib
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rm -vrf lib/pixmaps
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ln -vs $shareddir/lib/pixmaps $out/lib/pixmaps
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chmod a+rwx -R $shareddir/lib/pixmaps
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# bulk copy
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# bulk copy
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cp -vau * $out
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cp -vau * $out
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# replace arb script
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# replace arb script
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@ -48,9 +55,10 @@ stdenv.mkDerivation {
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#!/bin/sh
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#!/bin/sh
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echo Starting Nix compiled arb from $out
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echo Starting Nix compiled arb from $out
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echo Shared databases are located in $datadir
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echo Shared databases are located in $shareddir
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# sometimes local profiles override these:
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export ARBHOME=$out
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export ARBHOME=$out
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export LD_LIBRARY=$ARBHOME/lib
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export LD_LIBRARY=$ARBHOME/lib
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$out/bin/arb_ntree $*
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$out/bin/arb_ntree $*
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@ -60,9 +68,10 @@ ARB
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meta = {
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meta = {
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description = "ARB software for sequence database handling and analysis";
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description = "ARB software for sequence database handling and analysis";
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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'';
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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.'';
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license = "non-free";
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license = "non-free";
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pkgMaintainer = "Pjotr Prins";
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pkgMaintainer = "http://BioLib.open-bio.org/";
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homepage = http://www.arb-home.de/;
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homepage = http://www.arb-home.de/;
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priority = "10"; # because it includes binaries of clustal etc.
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};
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};
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}
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}
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