4ab58fc7f3
commit 74c0e9192e17d9dfce50f811fdb7e82a2785134e
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:33:39 2008 +0200
Merge
commit ad91fb07a47226ed9e99f2dcb55b69ea0e70aa84
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:23:20 2008 +0200
openmotif: added some comments on license and download
commit 68a552975f5c7e0964c7c9625e08de0864757255
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:10:49 2008 +0200
Match parameters so arb starts compiling against openmotif
commit 16c52fb4071193f89acf6f7f53cfeff322285555
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 16:04:06 2008 +0200
Added openmotif package
commit 75c4bba418f16859e99e97f48785e27ad87e99f5
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 15:20:55 2008 +0200
Adding openmotif
commit 83a847d194b007e2ef856f2a5ad7c49939b6cf8c
Merge: 52918f1... 5ba4f06...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Tue Oct 7 14:15:05 2008 +0200
Merge branch 'syncsvn'
Conflicts:
pkgs/top-level/all-packages.nix
commit 52918f1f3af55429cc80c99d695e4a8d8b7869b0
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 18:31:06 2008 +0200
arb: Removed xfig as dependency (will add later)
arb: Don't recurse chmod settings of shared dir
commit c283733782dcbf0dcd88710e83f3eededf8f0866
Merge: e434cdf... a51773a...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 17:09:42 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit a51773a3d4295d7ce16e6a7e983ded814180e30a
Merge: 290ae0b... 241012c...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 16:54:14 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit e434cdf9b9acefab4f54e18204ff16af179c442d
Merge: ef57566... 241012c...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 16:12:27 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit 241012cae194d0f770be2224b5bb18b66e3ae0f0
Author: Pj <wrk@bio03.(none)>
Date: Mon Oct 6 16:11:11 2008 +0200
Added older version of lesstif for arb
commit 290ae0b802285a8dda41b3c5730e53239d73b47c
Merge: dfdf7fe... 53b6ceb...
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 15:20:17 2008 +0200
Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr
commit dfdf7fe8ac9599ec372bdb83630a236f227ad7d5
Author: Pjotr <pjotr.public05@thebird.nl>
Date: Mon Oct 6 15:15:04 2008 +0200
Fixed missing parameters for arb - and added kernelHeaders_2.6.18
commit ef57566834eb786cdcb57a799b7d1cb284eee389
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date: Mon Oct 6 15:06:26 2008 +0200
Changed arb permissions and priority
svn path=/nixpkgs/trunk/; revision=12985
78 lines
2.6 KiB
Nix
78 lines
2.6 KiB
Nix
args: with args;
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# NOTE: This package does not build on 64-bit systems. Because of some faulty
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# int->pointer arithmatic. The build scripts are abnormal - but it appears to
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# work.
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stdenv.mkDerivation {
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name = "arb-2007-Dec-07";
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src = fetchurl {
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url = http://download.arb-home.de/release/2007_12_07/arbsrc.tgz;
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sha256 = "04l7qj0wigg1h56a9d70hxhdr343v3dg5dhqrc7fahc1v4h8f1rd";
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};
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patches = [ ./makefile.patch ];
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buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv gnuplot ];
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unpackPhase = ''
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tar xzf $src
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'';
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buildPhase = ''
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echo `make` # avoids error signal
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export ARBHOME=`pwd`
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export PATH=$ARBHOME/bin:$PATH
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make all
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'';
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installPhase = ''
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ensureDir $out/lib
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shareddir=/nix/var/lib/arb
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# link out writable shared location lib/pts
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ensureDir $shareddir/lib/pts
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cp -vau lib/pts $shareddir/lib
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rm -vrf lib/pts
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ln -vs $shareddir/lib/pts $out/lib/pts
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chmod a+rwx $shareddir/lib/pts
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# link out writable shared location lib/nas/
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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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ln -vs $shareddir/lib/nas $out/lib/nas
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chmod a+rwx $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 $shareddir/lib/pixmaps
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# bulk copy
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cp -vau * $out
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# replace arb script
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mv $out/bin/arb $out/bin/arb.orig
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cat > $out/bin/arb << ARB
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#!/bin/sh
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echo Starting Nix compiled arb from $out
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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 LD_LIBRARY=$ARBHOME/lib
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$out/bin/arb_ntree $*
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ARB
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chmod +x $out/bin/arb
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'';
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meta = {
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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. Note that this package includes its own older versions of clustal etc.'';
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license = "non-free";
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pkgMaintainer = "http://BioLib.open-bio.org/";
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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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