gbrowse volvox Internal Server Error

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gbrowse volvox Internal Server Error

gbrowse learning
Dear Sir:
This is my first time using gbrowse, create volvox but encountered Internal Server Error in the tutorial guidance, the following is my Apache server error log:

Sun Jun 01 02:30:22 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
DBD::SQLite::db selectrow_array failed: no such table: session at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserDB.pm line 406.
DBD::SQLite::db selectrow_array failed: no such table: session at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserDB.pm line 447.
DBD::SQLite::db selectcol_arrayref failed: no such table: uploads at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 112.
Can't use an undefined value as an ARRAY reference at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 113.
[Sun Jun 01 02:33:51 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse

I would be very grateful for your answer, looking forward to your reply !



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Re: gbrowse volvox Internal Server Error

Scott Cain
Hello,

It looks to me like something went wrong with the installation of GBrowse.  Does the yeast sample database work?  If not, please try reinstalling GBrowse and watch for errors during the installation.

Another possibility is that permissions weren't set appropriately during the installation, which can be fixed without reinstalling.  Unfortunately, I can't tell from your error log what OS you're running, but if you look in the directory where flatfile databases go (typically /var/lib/gbrowse2, but it could be other places too), you should see a sessions directory, and it should be owned by the same user that owns apache (again, varies by OS, but is typically something like www-data, apache, or nobody).  If you see the directory but isn't owned by the apache owner, you can do this:

  sudo chown -R www-data:www-data sessions

where you would have to replace www-data with the name of the apache owner if it's different.

Scott



On Sat, May 31, 2014 at 2:56 PM, gbrowse learning <[hidden email]> wrote:
Dear Sir:
This is my first time using gbrowse, create volvox but encountered Internal Server Error in the tutorial guidance, the following is my Apache server error log:

Sun Jun 01 02:30:22 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
DBD::SQLite::db selectrow_array failed: no such table: session at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserDB.pm line 406.
DBD::SQLite::db selectrow_array failed: no such table: session at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserDB.pm line 447.
DBD::SQLite::db selectcol_arrayref failed: no such table: uploads at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 112.
Can't use an undefined value as an ARRAY reference at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 113.
[Sun Jun 01 02:33:51 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse

I would be very grateful for your answer, looking forward to your reply !



------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
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