[BioSQL-l] RE: [Gmod-gbrowse] Re: gbrowse on top of biosql
Marc Logghe
Marc.Logghe at devgen.com
Mon Jan 24 17:19:58 EST 2005
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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