[BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql
Hilmar Lapp
hlapp at gnf.org
Tue Jan 25 12:36:12 EST 2005
This is a weird error. Just wanted to say thanks to everybody who
chipped in and helped out, and special thanks to Marc for following
this through. -hilmar
On Jan 25, 2005, at 7:05 AM, Genevieve DeClerck wrote:
> 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
>> > -------------------------------------------------------------
>> >
>> >
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive
>> Reporting
>> Tool for open source databases. Create drag-&-drop reports. Save time
>> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
>> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------
More information about the BioSQL-l
mailing list