[BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql
Genevieve DeClerck
gad14 at cornell.edu
Tue Jan 25 10:05:55 EST 2005
Marc,
When I loaded the sample parkin data here are the commands i used:
bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname
biosql -dbpass XXXXXX -namespace genbank -format fasta
~/downloads/bioperl-db/t/data/parkin.fasta
bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname
biosql -dbpass XXXXXX -namespace genbank -format genbank
~/downloads/bioperl-db/t/data/parkin.gb
I added 'namespace genbank' to the db_args definition in my conf file
and retried gbrowse. This time when I Search for AB019558 I get an
"Internal Server Error" (default white html page). Here's what my http
error file has:
Can't locate object method "class" via package
"Bio::DB::Das::BioSQL::Segment" at
/Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser.pm
line 1682.
[Tue Jan 25 10:00:29 2005] [error] [client 132.XX.XX.XX] Premature end
of script headers: /Library/WebServer/CGI-Executables/gbrowse
I tried, for the heck of it, setting namespace to 'bioperl' too - with
this the gbrowse ref font "is not recognized" error returns.
-Genevieve
Marc Logghe wrote:
> Hi Genevieve,
> the error you mention is the one you get when the namespace is not set in the conf.
> It should read:
> db_args = driver mysql
> dbname biosql
> biodbname genbank
> host localhost
> user nobody
> pass ""
> namespace <your_namespace>
>
> A bioentry search in BioSQL needs a namespace. When you did not provide it explicitely while populating biosql it is probably the default 'bioperl'.
> HTH,
> Marc
>
>
>
> -----Oorspronkelijk bericht-----
> Van: gmod-gbrowse-admin at lists.sourceforge.net namens Genevieve DeClerck
> Verzonden: ma 24-1-2005 18:44
> Aan: biosql-l at open-bio.org; hlapp at gnf.org; gmod-gbrowse at lists.sourceforge.net; lstein at cshl.edu
> Onderwerp: [Gmod-gbrowse] Re: gbrowse on top of biosql
>
> Thanks for the responses Hilmar, Marc and Lincoln.
> Since biosql and gbrowse 1.62 should be working together, I
> suspect my problem might be config related. I can get the front GBrowse
> page to display in web browser, but when I enter a Landmark or Region in
> the search box (e.g. AB019558) and Search, a GBrowse error message in
> bold red font at the top of the page: "The landmark named AB019558 is
> not recognized. See the help pages for suggestions." AB019558 is the
> accession number of the feature I loaded into this test database (from
> bioperl-db/t/data/parkin.gb) so it should be found.
>
> Here's what the httpd error log has (many lines of this repeated. One for
> each of my Search attempts on biosql gbrowse page):
>
> Use of uninitialized value in concatenation (.) or string at
> /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm
> line 116.
>
> Line 116 is inside of sub fetch_Seq_by_accession. It looks like a
> BioQuery object cannot be made because an argument is missing?
>
> I've tried many combinations of likely "Region" or "Location" names and
> coordinates using data loaded into the db in seqfeature and location
> tables... but always get the "not recognized" error.
>
> The conf file I have is basically a copy of 06.biosql.conf.. except for
> the first, [GENERAL], stanza where I put in my info. The 'pass' field
> could be a problem - i have '', while, 06.biosql.conf has a string
> (xyzzy) -- but I was under the impression that you don't set a password
> in mysql for user 'nobody.' This is setup I have for the other
> non-biosql gbrowse-mysql databases I'm running. Besides, I experimented
> with this by setting a password for 'nobody' in mysql and entered the
> password in my biosql.conf file in the 'pass' field in [General]. All it
> did was break my other gbrowse-mysql db's which don't use passwords for
> nobody - it had no effect on the gbrowse-biosql db - still getting "not
> recognized" error when Searching...
>
> I figure this might be a good time to post the contents of my
> biosql.conf file.. see below. I thought of providing a dump of my biosql
> database (which was simply loaded with test data from
> biopero-db/t/data/parkin.gb) but I'm not sure how helpful that would be..
>
> Thanks for all your help,
> Genevieve
>
> #***********************************************
> # originated from 06.biosql.conf
> (http://darwin.biochem.okstate.edu/gbrowse/contrib/conf_files/06.biosql.conf)
> [GENERAL]
> description = BioSQL
> db_adaptor = Bio::DB::Das::BioSQL
> db_args = driver mysql
> dbname biosql
> biodbname genbank
> host localhost
> user nobody
> pass ""
>
> plugins = SequenceDumper FastaDumper RestrictionAnnotator
>
> # Web site configuration info
> stylesheet = /gbrowse/gbrowse.css
> buttons = /gbrowse/images/buttons
> tmpimages = /gbrowse/tmp
>
> # where to link to when user clicks in detaild view
> link = http://localhost/gbrowse?ref=$ref;start=$start;stop=$end
>
> # what image widths to offer
> image widths = 450 640 800 1024
>
> # default width of detailed view (pixels)
> default width = 800
> default features = CDS
> repeat_region
>
> # max and default segment sizes for detailed view
> max segment = 500000
> default segment = 50000
>
> # zoom levels
> zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000
> 500000 1000000
> low res = 200000
>
> # colors of the overview, detailed map and key
> overview bgcolor = wheat
> detailed bgcolor = white
> key bgcolor = beige
>
> footer = <hr>
> <table width="100%">
> <TR>
> <TD align="LEFT" class="databody">
> For the source code for this browser, see the <a
> href="http://www.gmod.org">
> Generic Model Organism Database Project.</a> For other questions, send
> mail to <a href="mailto:lstein at cshl.org">lstein at cshl.org</a>.
> </TD>
> </TR>
> </table>
> <hr>
> <pre>$Id: 06.biosql.conf,v 1.7 2003/06/26 12:32:23 lstein dead $</pre>
>
> # examples to show in the introduction
> examples = AB019558
>
> # "automatic" classes to try when an unqualified identifier is given
> automatic classes = Accession
>
> [TRACK DEFAULTS]
> glyph = generic
> height = 8
> bgcolor = cyan
> fgcolor = cyan
> fontcolor = black
> font2color = blue
> label density = 25
> bump density = 100
>
> ################################################################################
> # the remainder of the sections configure particular features to sho
> ################################################################################
>
> [CDS]
> feature = CDS
> glyph = transcript2
> #glyph = generic
> bgcolor = turquoise
> fgcolor = black
> height = 10
> connector = solid
> label = sub {
> my $feature = shift;
> warn "feature = $feature";
> my @tags = $feature->each_tag_value('cds_id');
> $tags[0];
> }
> description = sub {
> my $feature = shift;
> warn "feature = $feature";
> my @tags = $feature->each_tag_value('gene_id');
> warn "tag = $tags[0]";
> $tags[0];
> }
> # key = Predicted transcripts
>
> [REPEAT]
> feature = repeat_region
> glyph = generic
> bgcolor = red
> height = 10
> description = 1
> key = Repeat regionss
>
> [TranslationF]
> glyph = translation
> global feature = 1
> frame0 = cadetblue
> frame1 = blue
> frame2 = darkblue
> height = 20
> fgcolor = purple
> strand = +1
> translation = 3frame
> key = 3-frame translation (forward)
>
> [DNA/GC Content]
> glyph = dna
> global feature = 1
> height = 40
> do_gc = 1
> fgcolor = red
> axis_color = blue
>
> [TranslationR]
> glyph = translation
> global feature = 1
> frame0 = darkred
> frame1 = red
> frame2 = crimson
> height = 20
> fgcolor = blue
> strand = -1
> translation = 3frame
> key = 3-frame translation (reverse)
>
> #***********************************************
>
> --
>
> >> The adaptor you want is Bio::DB::Das::BioSQL. Once you install
> >> GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the
> >> parameters you need to pass in the conf file. Also see
> >> contrib/conf/06.biosql.conf for an example.
> >>
> >> There is also a BIOSQL HOWTO in the pod documentation. It seems to be
> >> unecessarily pessimistic, saying that "the biosql adaptor is not
> >> known to work."
> >>
> >> One thing I just noticed, is that there is a typo in the example conf
> >> file. It says the adaptor is Bio::DB::BioSQL, but it should be
> >> Bio::DB::Das::BioSQL.
> >>
> >> Lincoln
>
>
>
> Marc Logghe wrote:
> >>It is possible. There were even benchmarks run for gbrowse against
> >>dbgff, chado, and biosql. Gbrowse will need a special adaptor
> >>that was
> >>written and tested by Simon at CSHL last year. I'm not sure whether
> >>this was included in the last gbrowse release, but the folks at the
> >>gbrowse mailing list can probably help you out
> >
> >
> > I can confirm this. Don't know what is the situation now, but it
> _used_ to work with version 1.61.
> >
> >
> >>>have not been successfully as of yet.
> >
> >
> > Genevieve, could you elaborate on that ? Do you see error messages ?
> Is there a problem of configuration ?
> >
> > Marc
> >
> >
> >
> > It is possible. There were even benchmarks run for gbrowse against
> dbgff, chado, and biosql. Gbrowse will need a special adaptor that was
> written and tested by Simon at CSHL last year. I'm not sure whether this
> was included in the last gbrowse release, but the folks at the gbrowse
> mailing list can probably help you out.
> >
> > -hilmar
> >
> > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote:
> >
> >> Hi,
> >>
> >> I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql,
> on OS
> >> X) and successfully loaded some sample data (parkin.fasta,
> parkin.gb). I'm
> >> now trying to get this biosql database to work with gbrowse (1.62), but
> >> have not been successfully as of yet. From what I've gathered from
> >> scanning the BioSQL-l archives and from various google searches, it may
> >> not be possible to view a biosql database with gbrowse yet. Is this
> true?
> >>
> >> Thanks,
> >> Genevieve
> >>
> >> _______________________________________________
> >> BioSQL-l mailing list
> >> BioSQL-l at open-bio.org
> >> http://open-bio.org/mailman/listinfo/biosql-l
> >>
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> >
>
>
>
>
>
>
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