Re: FW: Fixing track loading/sessions problem

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Re: FW: Fixing track loading/sessions problem

Christopher Porter

Another data point. Upgraded to 2.08 this morning (from an early GB2 release) and had problems with track rendering. Replaced GBrowse.conf with .new and added back my data sources as Joseph suggested, but couldn't get any tracks to display (just the ruler). Then followed Abby's suggestion and set 'user_account_db = memory' (although user accounts = 0) - tracks are now displaying properly.

Server is running on RHEL5.

Chris

-------------------------------------------
From: Abigail Cabunoc[[hidden email]]
Sent: Thursday, May 13, 2010 5:17:47 PM
To: Lincoln Stein; joseph franklin

Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Fixing track loading/sessions problem
Auto forwarded by a Rule


Hi Lincoln,

 

We had a similar problem, the custom tracks weren’t working properly until we set user_account_db = memory in GBrowse.conf.  We hadn’t set user accounts to anything.

 

Abby

 


From: Lincoln Stein [mailto:[hidden email]]
Sent: Thursday, May 13, 2010 4:41 PM


To: joseph franklin
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Fixing track loading/sessions problem

 

There's no reason that this should affect anything. user_account_db is not consulted if user accounts is set to false. So I am mystified. Let me know if anything like this happens again.

 

Lincoln

On Thu, May 13, 2010 at 12:42 PM, joseph franklin <[hidden email]> wrote:

Never mind, I replaced my GBrowse.conf file with the default and added my data sources back in and the tracks are loading again.  I'm still not sure what was causing the problem with the session locks, because the only line that was different from default was the "user_account_db" variable setting, and the "user accounts" variable was 0.  Hopefully this solution helps someone else down the line.
Joe


On 13 May 2010, at 9:09, joseph franklin wrote:

> I wrote a few days ago about a problem I'm having with Gbrowse2 (latest from svn) that appears to be related to my corrupting the session locks.  Tracks load properly when they are first loaded, but fail to refresh when a new genomic location is selected.  There appear to be no relevant errors in the apache2 log (see previous message below).  Lincoln suggested that I reset my session, or clear out the sessions directory.  I've done both, restarted apache2, and now sometimes get the error in the browser: "Can't call method "Flush" without a package or object reference."
>
> Does anyone have suggestions for recovering from this type of problem?
>
>
>
>
>
> -------------------------------------------
>
> Perhaps this helps: I'm now getting an error in the browser: "Can't call method "Flush" without a package or object reference."
>
> -Joe
>
>
> ___________________________
> Hi,
>
> I have a problem that I've been unable to troubleshoot.  Gbrowse (2.04) was working fine.  Now, the browser page loads correctly, and tracks appear properly rendered when you turn them on.  However, upon moving to a new genomic region, the tracks on the page do not reload, but remain as gray-boxes.  Turning on a new track works fine, but that track will fail to refresh upon moving to a new region as well.  The rotating "working" indicator in the upper left corner is constantly active.
>
> The apache2 error log contains nothing but two errors, repeated:
> Use of uninitialized value $rows in split at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render/HTML.pm line 925.
> Use of uninitialized value $cols in split at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render/HTML.pm line 927.
>
> These are in the sub category_table function so don't seem related.
>
> It seems like some sort of caching problem (?).  Though I was messing with the session lock section of GBrowse.conf (for no good reason, really), I've returned everything in that section to default and restarted apache2.
>
> Thanks again for any suggestions on fixing this.
> Joe Franklin
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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