Re: [Gmod-gbrowse] Missing Details panel in GBrowseSyn

[Sheldon M. <she...@gm...>]

GBrowse on CPAN does not have the latest patches.  You will want to get
GBrowse and re-install.
Things may get messy if you mix CPAN and the git version, so I would purge
(except your data) before the update.

$ git clone https://github.com/GMOD/GBrowse.git
$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install

Sheldon


On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <mu...@uw...> wrote:

> Hi Sheldon,
>
> I went digging through some forums and found that I was running an old
> version of gbrowse.  I purged reisntalled and now I'm getting an apache
> error that an environment variable isn't set properly.  Another forum dive
> found this thread:
> http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
> where you say to do a fresh git pull to fix things.  I did a git clone of
> the GBrowse repository as outlined here:
> http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
> But that didn't get it to load, Unfortunately, I installed the latest
> version via CPAN and I'm new to git commands.  What is the repository I
> need to point git pull at to update the environment variable correctly?
>
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
> On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model
> Organism System Database] <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=5712727&i=0>> wrote:
>
>> Hi Seth,
>>
>> Thanks for providing all of the information with your request.  One thing
>> I notice is that your GFF reference sequence names are using a hyphen
>> (Chr08_1-14305), while your alignment data uses an underscore
>> (Chr08_1_14305).  Mis-matched refseq names break the linkage between the
>> GFF and the alignment data.  If I recall correctly, gbrowse_syn will not
>> display a details panel if there are no alignment data found.  I would
>> recommend changing the GFF refseq names to also use the underscore.  I
>> think a hyphen could potentially confuse the parser that extracts meta-data
>> from the refseq ID in the alignment file.
>>
>> If you are still stuck, could you send an excerpt of your apache error
>> log?
>>
>>
>> Sheldon McKay
>>
>>
>> On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]
>> <http://user/SendEmail.jtp?type=node&node=5712726&i=0>> wrote:
>>
>>> Hello Everyone,
>>>
>>> I'm trying to configure GBrowseSyn on our webserver and figured I'd
>>> start small scale to learn my way around.  I isolated one scaffold from 2
>>> different genomes and found where they align, converted it to a clustalw
>>> format then uploaded it to a mysql database using
>>> gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the
>>> provided *O.sativa* synconf, conf, and gff3 files as a base and
>>> modified them to match my dataset.  I can open GBrowseSyn in a browser
>>> pointed at localhost, I can even highlight the areas that I know match, but
>>> no matter what I do the Details panel doesn't load.  All I get are
>>> Instructions, Search, Overview, and Display_Settings.  I've attached my
>>> synconf, conf, and gff3, and the clustalw files.  Any suggestions on where
>>> I should look to try and get the details Panel to appear?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: (519) 253-3000 Ext: 4755
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Want excitement?
>>> Manually upgrade your production database.
>>> When you want reliability, choose Perforce
>>> Perforce version control. Predictably reliable.
>>>
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>>>
>>>
>>
>> ------------------------------------------------------------------------------
>>
>> Want excitement?
>> Manually upgrade your production database.
>> When you want reliability, choose Perforce
>> Perforce version control. Predictably reliable.
>>
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> ------------------------------------------------------------------------------
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> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
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