[Gmod-help] Re: [Gmod-gbrowse] gbrowse v2 and blast graphics tool

[Alessandra]

Hi all,

I tested this url:
http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720;add=NC_000913
BLASTN HSP1 661..720;

next url works:
http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720;

when I run this url:
http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720;add=NC_000913
BLASTN HSP1 661..720;

I have got these apache error log:

Use of uninitialized value $proposed_source in exists at
/usr/local/lib/perl/5.10.0/Bio/Graphics/Browser.pm line 258.
[Fri Sep 18 23:34:03 2009] [error] Not an ARRAY reference at
/usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 1673.\n

I use v1.995 release. Next weekend I will test this url with last version.
I hope that this could be an help.
Best,
Alessandra.


On Fri, Sep 18, 2009 at 8:04 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Lincoln, (and the rest of the list)
>
> Shuai hasn't had a chance to look at using BLAST Graphic Viewer in
> GBrowse 2.  Do you know enough about the viewer to expect that it
> would be broken in GBrowse 2?  I'm trying to figure out if Alessandra
> should keep working on trying to get this to work, or if BLAST Graphic
> Viewer just won't work with GBrowse 2 until it is upgraded.
>
> Has anyone got the BLAST graphic viewer to work with GBrowse 2?
>
> Thanks,
>
> Dave C.
>
> On Fri, Sep 18, 2009 at 10:53 AM, Shuai Weng <shuai at genome.stanford.edu> wrote:
>>
>> Hi Dave,
>>
>> Sorry, I didn't get chance to do anything with BLAST Graphic Viewer
>> recently.
>>
>> Shuai
>>
>> On Fri, 18 Sep 2009, Dave Clements, GMOD Help Desk wrote:
>>
>>> Hi Shuai,
>>>
>>> Has there been any work done to test the BLAST Graphic Viewer with GBrowse
>>> 2?
>>>
>>> Thanks,
>>>
>>> Dave C.
>>>
>>> On Thu, Sep 17, 2009 at 10:20 AM, Alessandra
>>> <alessandra.bilardi at gmail.com> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I'm testing blast graphics 0.02 tool with gbrowse v2.
>>>> so that I discovered that old paths didn't work with gbrowse v2.
>>>> this is an example that with gbrowse v1.68 worked:
>>>>
>>>>
>>>> http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/?ref=chr15_random;start=1592829;stop=1596888;add=chr15_random%20BLASTN%20HSP4%201594829..1594888;h_region=chr15_random:1594829..1594888;
>>>>
>>>> Can you help me about it?
>>>>
>>>> Alessandra.
>>>>
>>>>
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>>>
>>>
>>>
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>>
>
>
>
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-- 
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 Via Ugo Bassi, 58/B - 35121 Padova
 Tel +390498276165 Fax +390498276159
  http://www.linkedin.com/in/bilardi
----
La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
Keep simple, stupid (KISS, IT)
----