issues with eneric Genome Browser Version 2 tutorial for administrators

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issues with eneric Genome Browser Version 2 tutorial for administrators

Patricia Angelica Vera

Dear GBrowse support staff,


I'm trying to work on the Genome Browser Version 2 tutorial and I'm having issues in the 1. "The Basics section", I can not visualize de data set on the web browser, when I type ctgA in the search box I got a "Not Found" message.

I tried the troubleshooting that is under and I can not find the yeast.conf file on my directory:


/var/www/gbrowse2/tutorial/conf_files


The other seems be ok, I would appreciate a hint to keep going through the tutorial,


Thank you for your time,

Patricia


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Re: issues with eneric Genome Browser Version 2 tutorial for administrators

Scott Cain
Hi Patricia,

The yeast.conf file wouldn't be in the conf_files directory, as that directory is only for configuration files that are used in the tutorial.  Configuration files that are currently available to GBrowse are typically stored in /etc/gbrowse2; is the yeast.conf file there?  If not, perhaps something went wrong when you installed GBrowse.  How did you install it and what operating system are you using?

If it is there, what happens when you point your browser at


If that brings up a display, then there is presumably something wrong with the way you started out the tutorial.  Did you put the volvox.conf file in /etc/gbrowse2?  Did you put the remarks.gff file in /var/lib/gbrowse2/databases/volvox and make that volvox directory world readable?  Is there anything in the apache error log that might shed light on what is going wrong (the error log is typically in /var/log/apache2/error_log)?

That should be enough to get us started :-)

Scott



On Thu, Jul 24, 2014 at 1:57 AM, Patricia Angelica Vera <[hidden email]> wrote:

Dear GBrowse support staff,


I'm trying to work on the Genome Browser Version 2 tutorial and I'm having issues in the 1. "The Basics section", I can not visualize de data set on the web browser, when I type ctgA in the search box I got a "Not Found" message.

I tried the troubleshooting that is under and I can not find the yeast.conf file on my directory:


/var/www/gbrowse2/tutorial/conf_files


The other seems be ok, I would appreciate a hint to keep going through the tutorial,


Thank you for your time,

Patricia


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
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

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-gbrowse mailing list
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