Plugin problem when installing in Ubuntu VM

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Plugin problem when installing in Ubuntu VM

Marc Höppner-3
Hi,

this may be a trivial thing, or maybe not, but I am failing miserably to get WebApollo to work properly in an Lubuntu Virtual machine.

Setting up WA and loading a genome etc works fine,  but the Blat plugin doesn’t behave:

When navigating to ‘Tools’ on the front page, I get ‘No search plugins setup’

And on a config view, I don’t even get ‘Tools’.

The config/ directory contains what I consider a correctly filled out blat_config.xml and the blat executable

I use the same set up procedure on a production system (which however runs Scientific Linux), and as far as I can tell there isn’t anything obvious in the script that deploys the WebApollo code. Any suggestions where I should look for the issue?

Regards,

Marc
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Re: Plugin problem when installing in Ubuntu VM

nathandunn

In config.xml, you should have a section like this:

<sequence_search_tools>
   <!-- one <sequence_search_tool> element per tool -->
   <sequence_search_tool>
      <!-- display name for the search tool -->
      <key>BLAT nucleotide</key>
      <!-- class for handling search -->
      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineNucleotideToNucleotide</class>
      <!-- configuration for search tool -->
      <config>/config/blat_config.xml</config>
   </sequence_search_tool>

   <sequence_search_tool>
      <!-- display name for the search tool -->
      <key>BLAT protein</key>
      <!-- class for handling search -->
      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineProteinToNucleotide</class>
      <!-- configuration for search tool -->
      <config>/config/blat_config.xml</config>
   </sequence_search_tool>

</sequence_search_tools>


Nathan

On Oct 16, 2014, at 5:13 AM, Marc Höppner <[hidden email]> wrote:

> Hi,
>
> this may be a trivial thing, or maybe not, but I am failing miserably to get WebApollo to work properly in an Lubuntu Virtual machine.
>
> Setting up WA and loading a genome etc works fine,  but the Blat plugin doesn’t behave:
>
> When navigating to ‘Tools’ on the front page, I get ‘No search plugins setup’
>
> And on a config view, I don’t even get ‘Tools’.
>
> The config/ directory contains what I consider a correctly filled out blat_config.xml and the blat executable
>
> I use the same set up procedure on a production system (which however runs Scientific Linux), and as far as I can tell there isn’t anything obvious in the script that deploys the WebApollo code. Any suggestions where I should look for the issue?
>
> Regards,
>
> Marc


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Re: Plugin problem when installing in Ubuntu VM

Marc Höppner-3
Hi,

thanks for the help. Turns out it was a permission issue - I installed WebApollo with a user that belongs to the tomcat7 group, but apparently that wasn’t good enough…changing permissions to tomcat7:tomcat7 fixed it..oh well!

/Marc

On 16 Oct 2014, at 18:35, Nathan Dunn <[hidden email]> wrote:

>
> In config.xml, you should have a section like this:
>
> <sequence_search_tools>
>   <!-- one <sequence_search_tool> element per tool -->
>   <sequence_search_tool>
>      <!-- display name for the search tool -->
>      <key>BLAT nucleotide</key>
>      <!-- class for handling search -->
>      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineNucleotideToNucleotide</class>
>      <!-- configuration for search tool -->
>      <config>/config/blat_config.xml</config>
>   </sequence_search_tool>
>
>   <sequence_search_tool>
>      <!-- display name for the search tool -->
>      <key>BLAT protein</key>
>      <!-- class for handling search -->
>      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineProteinToNucleotide</class>
>      <!-- configuration for search tool -->
>      <config>/config/blat_config.xml</config>
>   </sequence_search_tool>
>
> </sequence_search_tools>
>
>
> Nathan
>
> On Oct 16, 2014, at 5:13 AM, Marc Höppner <[hidden email]> wrote:
>
>> Hi,
>>
>> this may be a trivial thing, or maybe not, but I am failing miserably to get WebApollo to work properly in an Lubuntu Virtual machine.
>>
>> Setting up WA and loading a genome etc works fine,  but the Blat plugin doesn’t behave:
>>
>> When navigating to ‘Tools’ on the front page, I get ‘No search plugins setup’
>>
>> And on a config view, I don’t even get ‘Tools’.
>>
>> The config/ directory contains what I consider a correctly filled out blat_config.xml and the blat executable
>>
>> I use the same set up procedure on a production system (which however runs Scientific Linux), and as far as I can tell there isn’t anything obvious in the script that deploys the WebApollo code. Any suggestions where I should look for the issue?
>>
>> Regards,
>>
>> Marc
>
>