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Diffstat (limited to 'pkgs/applications/science/biology/arb/default.nix')
-rw-r--r-- | pkgs/applications/science/biology/arb/default.nix | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix new file mode 100644 index 000000000000..d84d4f081c66 --- /dev/null +++ b/pkgs/applications/science/biology/arb/default.nix @@ -0,0 +1,68 @@ +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/; + }; +} |