global_timeout setting

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global_timeout setting

Matthew Conte
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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Re: global_timeout setting

Jayaraman, Pushkala

This is what I am guessing, the track that you are trying to view has a lot of data.

If that is the case, try viewing a smaller region or use the “hide” option that will only allow you to view a region if one zooms beyond a certain level.

If you would still like to view the large region, then try using the mod_fastcgi option..

Im guessing these may work.. but Im a beginner at Gbrowse2 myself..

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Matthew Conte [mailto:[hidden email]]
Sent: Thursday, May 20, 2010 10:35 AM
To: [hidden email]; [hidden email]
Subject: [Gmod-gbrowse] global_timeout setting

 

Hello,

 

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

 

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

 

Any ideas?

 

-Matt


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Re: global_timeout setting

Scott Cain
In reply to this post by Matthew Conte
Hi Matthew,

Could the pink timeout image be cached?  Try changing the boundaries a
little bit, because I think the global timeout setting should work
here.

Scott


On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:

> Hello,
> I'm trying to view a single track of some very large regions (15-30MB) with
> GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering
> error: timeout; try a smaller region" (screen shot attached).  To get around
> this problem I figured I could change the global_timeout setting in the main
> GBrowse.conf file to something like 360 instead of the default 60.  However,
> it still times out after 60 seconds after making this change.  I've also
> increased the Apache timeout and restarted apache, but that didn't help.
>  I'm not running any slave rendering and the only error I'm getting in my
> apache error log is:
> timeout at
> /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm
> line 1228.
> Any ideas?
> -Matt
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: global_timeout setting

Lincoln Stein
In reply to this post by Matthew Conte
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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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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Re: global_timeout setting

Matthew Conte
Hey guys,

Thanks for the help, it was nice to come back from lunch with so many suggestions.

Scott, I think you are half right about the caching.  The pink track rendering timeout image still displays after 60 seconds, but I can see that the perl process is still running beyond the 60 seconds.  If I wait for the process to finish and then change the boundaries slightly, then the pink timeout image goes away and I get the image that I'm looking for.  So at least I have a work around for now.

Lincoln, I will upgrade to 2.07 and I look forward to the Bio::DB::SeqFeature::Store improvement.

cheers,
Matt

On Thu, May 20, 2010 at 12:33 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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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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Re: global_timeout setting

Lincoln Stein
Hi Matt,

This is not the expected behavior!  The perl process should terminate the moment the timeout is hit.

What database adaptor are you using for this track, and what version of Perl and OS?

Lincoln

On Thu, May 20, 2010 at 12:54 PM, Matthew Conte <[hidden email]> wrote:
Hey guys,

Thanks for the help, it was nice to come back from lunch with so many suggestions.

Scott, I think you are half right about the caching.  The pink track rendering timeout image still displays after 60 seconds, but I can see that the perl process is still running beyond the 60 seconds.  If I wait for the process to finish and then change the boundaries slightly, then the pink timeout image goes away and I get the image that I'm looking for.  So at least I have a work around for now.

Lincoln, I will upgrade to 2.07 and I look forward to the Bio::DB::SeqFeature::Store improvement.

cheers,
Matt

On Thu, May 20, 2010 at 12:33 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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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]>




--
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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Re: global_timeout setting

Matthew Conte
Hi Lincoln,

I guess I was expecting the perl process to continue for up to 360 seconds (what I set global_timeout to) AND the pink track rendering error image to not show up for 360 seconds either.  However, the pink track rendering image shows up after only 60 seconds still.  So it seems the global_timeout setting is working for the perl process, but not for what is displayed.

I'm using Bio::DB::SeqFeature::Store with Perl 5.8.9 on Mac OS 10.6.

Thanks,
Matt

On Thu, May 20, 2010 at 12:56 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

This is not the expected behavior!  The perl process should terminate the moment the timeout is hit.

What database adaptor are you using for this track, and what version of Perl and OS?

Lincoln


On Thu, May 20, 2010 at 12:54 PM, Matthew Conte <[hidden email]> wrote:
Hey guys,

Thanks for the help, it was nice to come back from lunch with so many suggestions.

Scott, I think you are half right about the caching.  The pink track rendering timeout image still displays after 60 seconds, but I can see that the perl process is still running beyond the 60 seconds.  If I wait for the process to finish and then change the boundaries slightly, then the pink timeout image goes away and I get the image that I'm looking for.  So at least I have a work around for now.

Lincoln, I will upgrade to 2.07 and I look forward to the Bio::DB::SeqFeature::Store improvement.

cheers,
Matt

On Thu, May 20, 2010 at 12:33 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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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]>




--
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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Re: global_timeout setting

Lincoln Stein
Hi Matthew,

It sounds like the caching system is not respecting the global timeout. Could you go to the "Preferences" tab, turn off caching, and see if this makes a difference?

Lincoln

On Thu, May 20, 2010 at 1:03 PM, Matthew Conte <[hidden email]> wrote:
Hi Lincoln,

I guess I was expecting the perl process to continue for up to 360 seconds (what I set global_timeout to) AND the pink track rendering error image to not show up for 360 seconds either.  However, the pink track rendering image shows up after only 60 seconds still.  So it seems the global_timeout setting is working for the perl process, but not for what is displayed.

I'm using Bio::DB::SeqFeature::Store with Perl 5.8.9 on Mac OS 10.6.

Thanks,
Matt

On Thu, May 20, 2010 at 12:56 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

This is not the expected behavior!  The perl process should terminate the moment the timeout is hit.

What database adaptor are you using for this track, and what version of Perl and OS?

Lincoln


On Thu, May 20, 2010 at 12:54 PM, Matthew Conte <[hidden email]> wrote:
Hey guys,

Thanks for the help, it was nice to come back from lunch with so many suggestions.

Scott, I think you are half right about the caching.  The pink track rendering timeout image still displays after 60 seconds, but I can see that the perl process is still running beyond the 60 seconds.  If I wait for the process to finish and then change the boundaries slightly, then the pink timeout image goes away and I get the image that I'm looking for.  So at least I have a work around for now.

Lincoln, I will upgrade to 2.07 and I look forward to the Bio::DB::SeqFeature::Store improvement.

cheers,
Matt

On Thu, May 20, 2010 at 12:33 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

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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]>




--
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]>




--
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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Re: global_timeout setting

Matthew Conte
Hi Lincoln,

Turning off caching from the preferences tab doesn't seem to make a difference.

Thanks,
Matt

On Thu, May 20, 2010 at 1:19 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matthew,

It sounds like the caching system is not respecting the global timeout. Could you go to the "Preferences" tab, turn off caching, and see if this makes a difference?

Lincoln


On Thu, May 20, 2010 at 1:03 PM, Matthew Conte <[hidden email]> wrote:
Hi Lincoln,

I guess I was expecting the perl process to continue for up to 360 seconds (what I set global_timeout to) AND the pink track rendering error image to not show up for 360 seconds either.  However, the pink track rendering image shows up after only 60 seconds still.  So it seems the global_timeout setting is working for the perl process, but not for what is displayed.

I'm using Bio::DB::SeqFeature::Store with Perl 5.8.9 on Mac OS 10.6.

Thanks,
Matt

On Thu, May 20, 2010 at 12:56 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

This is not the expected behavior!  The perl process should terminate the moment the timeout is hit.

What database adaptor are you using for this track, and what version of Perl and OS?

Lincoln


On Thu, May 20, 2010 at 12:54 PM, Matthew Conte <[hidden email]> wrote:
Hey guys,

Thanks for the help, it was nice to come back from lunch with so many suggestions.

Scott, I think you are half right about the caching.  The pink track rendering timeout image still displays after 60 seconds, but I can see that the perl process is still running beyond the 60 seconds.  If I wait for the process to finish and then change the boundaries slightly, then the pink timeout image goes away and I get the image that I'm looking for.  So at least I have a work around for now.

Lincoln, I will upgrade to 2.07 and I look forward to the Bio::DB::SeqFeature::Store improvement.

cheers,
Matt

On Thu, May 20, 2010 at 12:33 PM, Lincoln Stein <[hidden email]> wrote:
Hi Matt,

I'm looking at the code here and it looks like "global_timeout" should work as expected. However this is one of those options that can be either in the GBrowse.conf file or in one of the data source config files, with the latter overriding the former. If caching isn't the issue, then perhaps you should look in the data source config file to see if there is an overriding option there.

A few things will help you with these timeouts:

  1. If you upgrade to GBrowse 2.07 (and Bio::Graphics 2.09), rendering has been made much more efficient by utilizing multiple CPUs; track rendering speed should be noticeably improved.
  2. Wait just a few more days, and then there will be a version of bioperl's Bio::DB:;SeqFeature::Store that will automatically go into "summary mode" when there are too many features to display. This will plot a nice histogram or density plot of your features across large regions.
  3. Change the display mode to "hide" if the region is too big to display (as noted in Pushkala's message)
  4. If you are displaying quantitative data, consider using the BigWig adaptor; it can display wiggle tracks of chromosome length.
Lincoln

On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
Hello,

I'm trying to view a single track of some very large regions (15-30MB) with GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering error: timeout; try a smaller region" (screen shot attached).  To get around this problem I figured I could change the global_timeout setting in the main GBrowse.conf file to something like 360 instead of the default 60.  However, it still times out after 60 seconds after making this change.  I've also increased the Apache timeout and restarted apache, but that didn't help.  I'm not running any slave rendering and the only error I'm getting in my apache error log is:

timeout at /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 1228.

Any ideas?

-Matt

------------------------------------------------------------------------------


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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]>




--
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]>




--
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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gbrowse2.08 problem

donghe
In reply to this post by Scott Cain
Hi Scott,

I installed gbrowse2.08 in my box. The installation did well. when I view
tracks, they give me this error "track rendering error: Can't call method
"prepare" on an undefined value at
/usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Das/Chado.pm line 1472..."

Any ideas?

Thanks

Dong





Hello,
> I'm trying to view a single track of some very large regions (15-30MB) with
> GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering
> error: timeout; try a smaller region" (screen shot attached).  To get
around
> this problem I figured I could change the global_timeout setting in the
main
> GBrowse.conf file to something like 360 instead of the default 60.
However,

> it still times out after 60 seconds after making this change.  I've also
> increased the Apache timeout and restarted apache, but that didn't help.
>  I'm not running any slave rendering and the only error I'm getting in my
> apache error log is:
> timeout at
> /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm
> line 1228.
> Any ideas?
> -Matt
> -------------------



















hink the global timeout setting should work

> here.
>
> Scott
>
>
> On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
>> Hello,
>> I'm trying to view a single track of some very large regions (15-30MB)
>> with
>> GBrowse 2.03 and after 60 seconds the track gives me the "Track
>> rendering
>> error: timeout; try a smaller region" (screen shot attached).  To get
>> around
>> this problem I figured I could change the global_timeout setting in the
>> main
>> GBrowse.conf file to something like 360 instead of the default 60.
>>  However,
>> it still times out after 60 seconds after making this change.  I've also
>> increased the Apache timeout and restarted apache, but that didn't help.
>>  I'm not running any slave rendering and the only error I'm getting in
>> my
>> apache error log is:
>> timeout at
>> /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm
>> line 1228.
>> Any ideas?
>> -Matt
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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Re: gbrowse2.08 problem

Scott Cain
Hi Dong,

You need to get a new version of Bio::DB::Das::Chado from CPAN.  That
was fixed in the 0.26 release.

Scott


On Thu, Jun 3, 2010 at 1:25 PM,  <[hidden email]> wrote:

> Hi Scott,
>
> I installed gbrowse2.08 in my box. The installation did well. when I view
> tracks, they give me this error "track rendering error: Can't call method
> "prepare" on an undefined value at
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Das/Chado.pm line 1472..."
>
> Any ideas?
>
> Thanks
>
> Dong
>
>
>
>
>
> Hello,
>> I'm trying to view a single track of some very large regions (15-30MB) with
>> GBrowse 2.03 and after 60 seconds the track gives me the "Track rendering
>> error: timeout; try a smaller region" (screen shot attached).  To get
> around
>> this problem I figured I could change the global_timeout setting in the
> main
>> GBrowse.conf file to something like 360 instead of the default 60.
> However,
>> it still times out after 60 seconds after making this change.  I've also
>> increased the Apache timeout and restarted apache, but that didn't help.
>>  I'm not running any slave rendering and the only error I'm getting in my
>> apache error log is:
>> timeout at
>> /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm
>> line 1228.
>> Any ideas?
>> -Matt
>> -------------------
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> hink the global timeout setting should work
>> here.
>>
>> Scott
>>
>>
>> On Thu, May 20, 2010 at 11:35 AM, Matthew Conte <[hidden email]> wrote:
>>> Hello,
>>> I'm trying to view a single track of some very large regions (15-30MB)
>>> with
>>> GBrowse 2.03 and after 60 seconds the track gives me the "Track
>>> rendering
>>> error: timeout; try a smaller region" (screen shot attached).  To get
>>> around
>>> this problem I figured I could change the global_timeout setting in the
>>> main
>>> GBrowse.conf file to something like 360 instead of the default 60.
>>>  However,
>>> it still times out after 60 seconds after making this change.  I've also
>>> increased the Apache timeout and restarted apache, but that didn't help.
>>>  I'm not running any slave rendering and the only error I'm getting in
>>> my
>>> apache error log is:
>>> timeout at
>>> /Library/Perl/5.8.9/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm
>>> line 1228.
>>> Any ideas?
>>> -Matt
>>> ------------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Bio::DB::Das::Chado update issue

donghe
Hi Scott,

I updated Bio::DB::Das::Chado(0.26) from CPAN,but when I run "perl
-MBio::DB::Das::Chado -e 'print $Bio::DB::Das::Chado::VERSION', it still
shows old version 0.11. what's wrong with it? how can I force Gb2 use new
version?

Thanks

Dong




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Re: Bio::DB::Das::Chado update issue

Scott Cain
Hi Dong,

That means that the old version of the Chado adaptor is still
installed somewhere in perl's search path.  When you install a new
version of a perl module, unless you have a good reason not to, you
should always include "UNINST=1" (for make based installs) or
"--uninst 1" (for Build based installs) to get rid of old modules.  If
you reinstall and provide this option to the install step, like this:

  sudo ./Build install --uninst 1

it should remove the old version of the Chado adaptor.

Scott


On Mon, Jun 28, 2010 at 1:47 PM,  <[hidden email]> wrote:

> Hi Scott,
>
> I updated Bio::DB::Das::Chado(0.26) from CPAN,but when I run "perl
> -MBio::DB::Das::Chado -e 'print $Bio::DB::Das::Chado::VERSION', it still
> shows old version 0.11. what's wrong with it? how can I force Gb2 use new
> version?
>
> Thanks
>
> Dong
>
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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install newest version of GBrowse

donghe
Hi Scott,

I meet a trouble to install the latest released version of GBrowse2, the
installation process always stuck on the following stage via either the
CPAN Shell or manually:

$ sudo ./Build test
.........
.........
.........
/etc/default/gbrowse-slave is already installed. New version will be
installed as /etc/default/gbrowse-slave.new
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
/etc/init.d/gbrowse-slave is already installed. New version will be
installed as /etc/init.d/gbrowse-slave.new
Creating include file for Apache config:
blib/etc/httpd/conf.d/z_gbrowse2.conf
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 108/138


Do you heave any idea for this problem?

Thanks

Dong









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Re: install newest version of GBrowse

Jayaraman, Pushkala
Hi,
I faced the same issue.. stop the installation delete all folders and
restart the installation.

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: [hidden email] [mailto:[hidden email]]
Sent: Tuesday, July 06, 2010 1:11 PM
To: Scott Cain
Cc: [hidden email]
Subject: [Gmod-gbrowse] install newest version of GBrowse

Hi Scott,

I meet a trouble to install the latest released version of GBrowse2, the
installation process always stuck on the following stage via either the
CPAN Shell or manually:

$ sudo ./Build test
.........
.........
.........
/etc/default/gbrowse-slave is already installed. New version will be
installed as /etc/default/gbrowse-slave.new
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
/etc/init.d/gbrowse-slave is already installed. New version will be
installed as /etc/init.d/gbrowse-slave.new
Creating include file for Apache config:
blib/etc/httpd/conf.d/z_gbrowse2.conf
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 108/138


Do you heave any idea for this problem?

Thanks

Dong









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Re: install newest version of GBrowse

donghe
Hi Pushkala,

I already deleted /etc/gbrowse2,/var/www/cgi-bin/gb2, and
/var/www/html/gbrowse2. what else do I have to remove?

Thanks

Dong

> Hi,
> I faced the same issue.. stop the installation delete all folders and
> restart the installation.
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
> Sent: Tuesday, July 06, 2010 1:11 PM
> To: Scott Cain
> Cc: [hidden email]
> Subject: [Gmod-gbrowse] install newest version of GBrowse
>
> Hi Scott,
>
> I meet a trouble to install the latest released version of GBrowse2, the
> installation process always stuck on the following stage via either the
> CPAN Shell or manually:
>
> $ sudo ./Build test
> .........
> .........
> .........
> /etc/default/gbrowse-slave is already installed. New version will be
> installed as /etc/default/gbrowse-slave.new
> Performing variable substitutions in blib/etc/init.d/gbrowse-slave
> /etc/init.d/gbrowse-slave is already installed. New version will be
> installed as /etc/init.d/gbrowse-slave.new
> Creating include file for Apache config:
> blib/etc/httpd/conf.d/z_gbrowse2.conf
> t/01yeast.t ............... ok
> t/02.rearchitecture.t ..... ok
> t/03.render.t ............. 108/138
>
>
> Do you heave any idea for this problem?
>
> Thanks
>
> Dong
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
> ------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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Re: install newest version of GBrowse

Lincoln Stein
In reply to this post by donghe
Didn't we have this issue before and it was resolved when the user deleted old versions of Bio::Graphics and BioPerl which were hanging around?

Lincoln

On Tue, Jul 6, 2010 at 2:10 PM, <[hidden email]> wrote:
Hi Scott,

I meet a trouble to install the latest released version of GBrowse2, the
installation process always stuck on the following stage via either the
CPAN Shell or manually:

$ sudo ./Build test
.........
.........
.........
/etc/default/gbrowse-slave is already installed. New version will be
installed as /etc/default/gbrowse-slave.new
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
/etc/init.d/gbrowse-slave is already installed. New version will be
installed as /etc/init.d/gbrowse-slave.new
Creating include file for Apache config:
blib/etc/httpd/conf.d/z_gbrowse2.conf
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 108/138


Do you heave any idea for this problem?

Thanks

Dong









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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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Re: install newest version of GBrowse

J.M.P. Alves
In reply to this post by donghe
Hi,

When I had that same problem, it was a conflict of different versions of
Perl modules (Bioperl and Graphics) installed, so the directories I
removed (actually, renamed) were under /usr/local/lib/perl/ -- it is an
older machine that had been update several times, and for some reason
different copies of GBrowse, Bioperl and Graphics were spread around
different places.

After that removal (and installing the newest libraries), I managed to
have both GBrowse 1 and 2 running in the same machine.

Cheers
J

[hidden email] wrote:

> Hi Pushkala,
>
> I already deleted /etc/gbrowse2,/var/www/cgi-bin/gb2, and
> /var/www/html/gbrowse2. what else do I have to remove?
>
> Thanks
>
> Dong
>
>> Hi,
>> I faced the same issue.. stop the installation delete all folders and
>> restart the installation.
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: [hidden email] [mailto:[hidden email]]
>> Sent: Tuesday, July 06, 2010 1:11 PM
>> To: Scott Cain
>> Cc: [hidden email]
>> Subject: [Gmod-gbrowse] install newest version of GBrowse
>>
>> Hi Scott,
>>
>> I meet a trouble to install the latest released version of GBrowse2, the
>> installation process always stuck on the following stage via either the
>> CPAN Shell or manually:
>>
>> $ sudo ./Build test
>> .........
>> .........
>> .........
>> /etc/default/gbrowse-slave is already installed. New version will be
>> installed as /etc/default/gbrowse-slave.new
>> Performing variable substitutions in blib/etc/init.d/gbrowse-slave
>> /etc/init.d/gbrowse-slave is already installed. New version will be
>> installed as /etc/init.d/gbrowse-slave.new
>> Creating include file for Apache config:
>> blib/etc/httpd/conf.d/z_gbrowse2.conf
>> t/01yeast.t ............... ok
>> t/02.rearchitecture.t ..... ok
>> t/03.render.t ............. 108/138
>>
>>
>> Do you heave any idea for this problem?
>>
>> Thanks
>>
>> Dong
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>> ------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
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--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: install newest version of GBrowse

Jayaraman, Pushkala
In reply to this post by Lincoln Stein

Yes,

If restarting the installation doesn’t work, deleting older versions of Bio::Perl definitely does work..

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, July 06, 2010 1:46 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] install newest version of GBrowse

 

Didn't we have this issue before and it was resolved when the user deleted old versions of Bio::Graphics and BioPerl which were hanging around?

 

Lincoln

On Tue, Jul 6, 2010 at 2:10 PM, <[hidden email]> wrote:

Hi Scott,

I meet a trouble to install the latest released version of GBrowse2, the
installation process always stuck on the following stage via either the
CPAN Shell or manually:

$ sudo ./Build test
.........
.........
.........
/etc/default/gbrowse-slave is already installed. New version will be
installed as /etc/default/gbrowse-slave.new
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
/etc/init.d/gbrowse-slave is already installed. New version will be
installed as /etc/init.d/gbrowse-slave.new
Creating include file for Apache config:
blib/etc/httpd/conf.d/z_gbrowse2.conf
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 108/138


Do you heave any idea for this problem?

Thanks

Dong










------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
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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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Re: install newest version of GBrowse

Jayaraman, Pushkala
In reply to this post by donghe
Hi Dong,
Are you installing this from cpan?
Like Lincoln said, remove the older versions of BioPerl if you
previously had gbrowse 1.7x setup... also read older emails from James P
Alves regarding the same issue..

If you are installing this from the svn repository make sure you delete
the "Generic Genome Browser" folder..
Start all over again. Download and install it once again. That should
work.

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: [hidden email] [mailto:[hidden email]]
Sent: Tuesday, July 06, 2010 1:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; Scott Cain; [hidden email]
Subject: RE: [Gmod-gbrowse] install newest version of GBrowse

Hi Pushkala,

I already deleted /etc/gbrowse2,/var/www/cgi-bin/gb2, and
/var/www/html/gbrowse2. what else do I have to remove?

Thanks

Dong

> Hi,
> I faced the same issue.. stop the installation delete all folders and
> restart the installation.
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
> Sent: Tuesday, July 06, 2010 1:11 PM
> To: Scott Cain
> Cc: [hidden email]
> Subject: [Gmod-gbrowse] install newest version of GBrowse
>
> Hi Scott,
>
> I meet a trouble to install the latest released version of GBrowse2,
the
> installation process always stuck on the following stage via either
the

> CPAN Shell or manually:
>
> $ sudo ./Build test
> .........
> .........
> .........
> /etc/default/gbrowse-slave is already installed. New version will be
> installed as /etc/default/gbrowse-slave.new
> Performing variable substitutions in blib/etc/init.d/gbrowse-slave
> /etc/init.d/gbrowse-slave is already installed. New version will be
> installed as /etc/init.d/gbrowse-slave.new
> Creating include file for Apache config:
> blib/etc/httpd/conf.d/z_gbrowse2.conf
> t/01yeast.t ............... ok
> t/02.rearchitecture.t ..... ok
> t/03.render.t ............. 108/138
>
>
> Do you heave any idea for this problem?
>
> Thanks
>
> Dong
>
>
>
>
>
>
>
>
>
>
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