Hi Greg,

 

I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user.

 

I could solve this by using 2 output files, but I don’t want to keep the history as concise as possible. To I found the option to use “display application”. I defined my as below:

 

<display id="sedmatreport" version="1.0.0" name="Show ">

    <link id="sedmatreport" name="SedMat_report">

        <url target_frame="galaxy_main">${BASE_URL}/static/prims/reports/${dataset.id}/sedmat_report.html</url>

    </link>

</display>

 

So in my tool config xml I have the following respective configuration:

 

       <command interpreter=" java -jar ">

           Mytool.jar

           ...some parameters....

       -outReport /galaxy-dist/static/prims/reports/$outputData.dataset.id/sedmat_report.html

        #end if         

       </command>

 

è  This works fine, but I would like to avoid using the static directory. Do you know if there is an alternative web directory configured by default in the Galaxy web-server?

è   

è  I also want to avoid the /galaxy-dist/ part in the tool configuration since the Galaxy home directory can vary. Is there a variable which I can use for this?

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

+31-317480891; skype: pieter.lukasse.wur

http://www.pri.wur.nl