Hi Franco,

The server error is thrown when your file named tool_data_table_conf.xml.sample 
is parsed.  The content of this file is the following.

 <!-- Locations of indexes in the bisulphite conversion -->
<table name="bismark_indexes" comment_char="#">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/bismark_indices.loc" />
</table>
<!-- Locations of bed files for bisulphite analysis -->
<table name="bismark_bed_files" comment_char="#">
        <columns>value, name, path</columns>
        <file path="tool-data/bismark_bed_files.loc" />
</table>

This is an invalid xml file because it requires a containing <tables> tag set 
since multiple <table> tag sets are defined.  

I've improved the current server error behavior by displaying an appropriate 
error message for this problem, but the fix will not make it out to the main 
Galaxy tool shed until the next Galaxy release, currently scheduled for about 
December 20.

In the meantime, I believe you should see better behavior if you upload a new 
version of this file to your repository that looks something like this:

<tables>
        <!-- Locations of indexes in the bisulphite conversion -->
        <table name="bismark_indexes" comment_char="#">
                <columns>value, dbkey, name, path</columns>
                <file path="tool-data/bismark_indices.loc" />
        </table>
        <!-- Locations of bed files for bisulphite analysis -->
        <table name="bismark_bed_files" comment_char="#">
                <columns>value, name, path</columns>
                <file path="tool-data/bismark_bed_files.loc" />
        </table>
</tables>

Thanks,

Greg Von Kuster


On Dec 3, 2012, at 6:40 PM, Franco Caramia wrote:

> Hi list, 
> 
> Trying to upload, delete, update files from a repository I own in the 
> toolshed I keep getting Server Error..
> 
> This is the repo: 
> http://fcara...@toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark
> 
> Is anyone having the same issues?? I could just delete the repository but no 
> option for that is given.. 
> 
> Thanks, 
> 
> Franco
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