The arb package (biology)

svn path=/nixpkgs/trunk/; revision=12956
This commit is contained in:
Pjotr Prins 2008-10-05 09:03:58 +00:00
parent 2391d84867
commit 29d6189e8b
2 changed files with 80 additions and 0 deletions

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args: with args;
# 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 x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ];
unpackPhase = ''
tar xzf $src
'';
buildPhase = ''
echo `make` # avoids error signal
export ARBHOME=`pwd`
export PATH=$ARBHOME/bin:$PATH
make all
'';
installPhase = ''
datadir=/nix/var/lib/arb
ensureDir $out/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 $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 $datadir/lib/nas $out/lib/nas
# 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 $datadir
export ARBHOME=$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'';
license = "non-free";
pkgMaintainer = "Pjotr Prins";
homepage = http://www.arb-home.de/;
};
}

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diff -r a1e04cdafd13 Makefile
--- a/Makefile Thu Sep 25 11:59:19 2008 +0200
+++ b/Makefile Thu Sep 25 11:59:27 2008 +0200
@@ -109,7 +109,7 @@ endif
ALLOWED_GCC_295_VERSIONS=2.95.3
ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3
-ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3
+ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.2.4
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)