[Gmod-help] RE: [Gmod-gbrowse] Gbrowse2 - Invoking URLs to view blast HSPs

[Naveed Ishaque (TSL)]

Sorry Dave, but this is the final email from me today. The full URL I use for adding tracks was:

http:/xxxxxxx/cgi-bin/gb2/gbrowse/hpa_emoy2_v8.3/?add=SuperContig0+blast_hit+example1+271700..272000
This leads to the 500 internal server error

http:/xxxxxxx/cgi-bin/gb2/gbrowse/hpa_emoy2_v8.3?add=SuperContig0+blast_hit+example1+271700..272000
The above leads to a refresh of the screen with no track being added

I've also tried out the code on other gbrowse2 servers and it seems to work - maybe there's a problem with our configuration or version of our gbrowse2? To let you know more about the version whenever we set up our  mysql database adapter, regardless of the username we provide in db_args, the mysql calls are made from user 'www-data'.

Thanks again, and no more emails from me today :)

Nav

-----Original Message-----
From: gmodhelp at googlemail.com [mailto:gmodhelp at googlemail.com] On Behalf Of Dave Clements, GMOD Help Desk
Sent: 11 February 2010 23:49
To: Naveed Ishaque (TSL)
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Gbrowse2 - Invoking URLs to view blast HSPs

Dear Nav,

I don't think this functionality was supposed to go away in GBrowse 2.

Can you send the exact URL you are using?  This will help with debugging.

Thanks,

Dave C.

On Tue, Feb 9, 2010 at 9:09 AM, Naveed Ishaque (TSL)
<Naveed.Ishaque at sainsbury-laboratory.ac.uk> wrote:
> Dear all,
>
>
>
> I would like to be able to display blast hits on gbrowse2 session. With
> gbrowse1.x I have been successful in using the "?add=..." (as in the Invoking
> URL section of the gbrowse HOWTO) parameter to display the HSPs but cannot
> use the same code with gbrowse2. Other URL invoking features like h_region
> seem to work and I'm wondering if I'm doing anything wrong.
>
>
>
> Also, would you recommend any other ways of displaying blast results onto
> gbrowse2? My current work flow is to perform a blast search on a server and
> generating a HTML file displaying the results which will contain links to
> the genome browser displaying the HSP as an "?add=..." parameter in the URL.
>
>
>
> Thanks,
>
>
>
> Nav
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



-- 
Please keep responses on the list!
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback