nixpkgs/pkgs/applications/science/biology/arb/default.nix

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{ stdenv, fetchurl, glew, mesa, libpng, lesstif, lynx, freeglut
, libtiff, rxp, sablotron, perl, jdk, transfig, gv, gnuplot, xorg }:
# NOTE: This package does not build on 64-bit systems. Because of some faulty
# int->pointer arithmatic. The build scripts are abnormal - but it appears to
# work.
stdenv.mkDerivation {
name = "arb-2007-Dec-07";
src = fetchurl {
url = http://download.arb-home.de/release/2007_12_07/arbsrc.tgz;
sha256 = "04l7qj0wigg1h56a9d70hxhdr343v3dg5dhqrc7fahc1v4h8f1rd";
};
patches = [ ./makefile.patch ];
buildInputs =
[ glew mesa libpng xorg.libXpm lesstif lynx freeglut libtiff rxp
sablotron xorg.libXaw perl jdk transfig xorg.libX11 xorg.libXext
xorg.libXt gv gnuplot
];
unpackPhase = ''
tar xzf $src
'';
buildPhase = ''
echo `make` # avoids error signal
export ARBHOME=`pwd`
export PATH=$ARBHOME/bin:$PATH
make all
'';
installPhase = ''
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
rm -vrf lib/pts
ln -vs $shareddir/lib/pts $out/lib/pts
Squashed commit of the following: 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
2008-10-07 16:35:11 +02:00
chmod a+rwx $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 $shareddir/lib/nas $out/lib/nas
Squashed commit of the following: 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
2008-10-07 16:35:11 +02:00
chmod a+rwx $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
Squashed commit of the following: 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
2008-10-07 16:35:11 +02:00
chmod a+rwx $shareddir/lib/pixmaps
# bulk copy
cp -vau * $out
# replace arb script
mv $out/bin/arb $out/bin/arb.orig
cat > $out/bin/arb << ARB
#!/bin/sh
echo Starting Nix compiled arb from $out
echo Shared databases are located in $shareddir
# sometimes local profiles override these:
export ARBHOME=$out
export LD_LIBRARY=$ARBHOME/lib
$out/bin/arb_ntree $*
ARB
chmod +x $out/bin/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.'';
license = "non-free";
pkgMaintainer = "http://BioLib.open-bio.org/";
homepage = http://www.arb-home.de/;
priority = "10"; # because it includes binaries of clustal etc.
};
}