diff options
| -rw-r--r-- | pkgs/applications/science/biology/arb/default.nix | 39 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 11 |
2 files changed, 17 insertions, 33 deletions
diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix index 5043462b81f2..d84d4f081c66 100644 --- a/pkgs/applications/science/biology/arb/default.nix +++ b/pkgs/applications/science/biology/arb/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation { patches = [ ./makefile.patch ]; - buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ]; + buildInputs = [glew mesa libpng x11 libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk ]; unpackPhase = '' tar xzf $src @@ -27,26 +27,19 @@ stdenv.mkDerivation { ''; installPhase = '' + datadir=/nix/var/lib/arb 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 + # 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 $shareddir/lib/pts $out/lib/pts - chmod a+rw -R $shareddir/lib/pts - # link out writable shared location lib/nas/ - ensureDir $shareddir/lib/nas - cp -vau lib/nas $shareddir/lib + 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 $shareddir/lib/nas $out/lib/nas - chmod a+rw -R $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 - chmod a+rw -R $shareddir/lib/pixmaps + ln -vs $datadir/lib/nas $out/lib/nas # bulk copy cp -vau * $out # replace arb script @@ -55,10 +48,9 @@ stdenv.mkDerivation { #!/bin/sh echo Starting Nix compiled arb from $out -echo Shared databases are located in $shareddir -# sometimes local profiles override these: +echo Shared databases are located in $datadir export ARBHOME=$out -export LD_LIBRARY=$ARBHOME/lib +export LD_LIBRARY=$ARBHOME/lib $out/bin/arb_ntree $* @@ -68,10 +60,9 @@ 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.''; + 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 = "http://BioLib.open-bio.org/"; + pkgMaintainer = "Pjotr Prins"; homepage = http://www.arb-home.de/; - priority = "10"; # because it includes binaries of clustal etc. }; } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 0953bcb39bca..3bd65a37abd5 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -4979,11 +4979,6 @@ let kernelHeaders = kernelHeaders_2_6_23; - kernelHeaders_2_6_18 = import ../os-specific/linux/kernel-headers/2.6.18.5.nix { - inherit fetchurl stdenv unifdef; - }; - - kernelHeaders_2_6_21 = import ../os-specific/linux/kernel-headers/2.6.21.3.nix { inherit fetchurl stdenv; }; @@ -7345,11 +7340,9 @@ let arb = import ../applications/science/biology/arb { inherit fetchurl stdenv readline libpng zlib x11 lesstif freeglut perl; - inherit (xlibs) libXpm libXaw libX11 libXext libXt; + inherit (xlibs) libXpm libXaw; # motif = lesstif; - inherit mesa glew libtiff lynx rxp sablotron jdk transfig; - # supporting tools - inherit gv xfig gnuplot; + inherit mesa glew libtiff lynx rxp sablotron jdk; }; biolib = import ../development/libraries/science/biology/biolib { |