Help with Gbrowse2 datasource conf file/GBrowse2.conf file errors.

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Help with Gbrowse2 datasource conf file/GBrowse2.conf file errors.

Jayaraman, Pushkala


I am trying to run a conf file from gbrowse1.7 onto Gbrowse2. I have made the necessary modifications such that the conf file can run on Gbrowse2.

But I seem to come across a 500 Internal server error.


Error logs show this:


[Mon May 24 12:39:43 2010] [error] [client] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/user/apache" and run the commands: "sudo mkdir .

inkscape .gnome2" and "sudo chown apache .inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file.

[Mon May 24 12:40:04 2010] [error] [client] The result of B::Deparse::coderef2text was empty - maybe you're trying to serialize an XS function?, at /usr/local/lib/

perl5/site_perl/5.8.8/Bio/Graphics/ line 443, referer:

[Mon May 24 12:40:04 2010] [error] [client] Premature end of script headers: gbrowse, referer:



Apart from the inkscape error what is B::Deparse::coderef2text? Please help me fix this..


Pushkala Jayaraman


Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229



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