Hi All, I did a non root local install of gbrowse in order to have multiple separate instances of gbrowse. The yeast_chr1 works fine (except for the concatenation of an initialized value warnings), but I cannot seem to get my chado database to work. I already have a root installed version of gbrowse on the machine that works fine, but I want to have separate versions to allow for development and production separation. The installation was done with Lincoln Steins modified makefile.pl (to get around the non-root access to /usr/bin) and with the following parameters:
CONF /home/asalbase/dev/conf HTDOCS /home/asalbase/dev/htdocs HTDOCS_REL / CGIBIN /home/asalbase/dev/cgi-bin LIB /home/asalbase/dev/perl-lib BIN /home/asalbase/dev/bin DO_XS 1 NONROOT 1 SELINUX 1 Any help would be greatly appreciated. The error I am getting is the following: ---------- ERROR ------------ [...] DBD::Pg::st execute failed: ERROR: missing FROM-clause entry for table "sub_f", referer: http://dev.asalbase.org/sal-bin/index [...] , referer: http://dev.asalbase.org/sal-bin/index [...] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://dev.asalbase.org/sal-bin/index [...] MSG: feature query failed, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Error::throw, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::DB::Das::Chado::Segment::_features2level /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/DB/Das/Chado/Segment.pm:1213, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::DB::Das::Chado::Segment::features /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/DB/Das/Chado/Segment.pm:737, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::DB::Das::Chado::Segment::new /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/DB/Das/Chado/Segment.pm:327, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::DB::Das::Chado::segment /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/DB/Das/Chado.pm:546, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::Graphics::Browser::_feature_get /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:2092, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: Bio::Graphics::Browser::name2segments /home/asalbase/dev/perl-lib/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:2032, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: main::lookup_features_from_db /home/asalbase/dev/cgi-bin/gbrowse:2004, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: main::get_features /home/asalbase/dev/cgi-bin/gbrowse:1898, referer: http://dev.asalbase.org/sal-bin/index [...] STACK: /home/asalbase/dev/cgi-bin/gbrowse:218, referer: http://dev.asalbase.org/sal-bin/index [...] -----------------------------------------------------------, referer: http://dev.asalbase.org/sal-bin/index [...] Premature end of script headers: gbrowse, referer: http://dev.asalbase.org/sal-bin/index ----------- END ERROR ------------------ keith ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-gbrowse mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
