problem integrating new jar file

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problem integrating new jar file

vijayalakshmi
Hi,

   I am trying to integrate a tool that is written in java into galaxy. The following is what I've done.

1) Created a directory inside /tools directory and put my xml and runnable jar file in it.
2) Linked the xml file in 'tool_conf.xml'.

tool_conf.xml

        <section name="sample tool" id="sample_tool">
<tool file="Sample/sample.xml"/>
</section>

sample.xml

        <tool id="sample" name="Compute correlation">
               <command>java -jar sample.jar</command>
        </tool>

sample.java (exported into a runnable jar file from eclipse)

         package Sample;
         public class Sample 
         {
         public static void main(String[] args)
         {
          System.out.println("Hello world this is important");
         }
         }

When I run the above, (i.e when I click on execute in the middle pane), nothing gets added to my current history. Since there is no visual output of any sort, I am not able to figure out where the problem lies. 

Any help or pointer is appreciated!
Thanks y'all!
VJ.


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Re: problem integrating new jar file

vs49
Hi,

   I am trying to integrate a tool that is written in java into galaxy. The following is what I've done.

1) Created a directory inside /tools directory and put my xml and runnable jar file in it.
2) Linked the xml file in 'tool_conf.xml'.

tool_conf.xml

        <section name="sample tool" id="sample_tool">
<tool file="Sample/sample.xml"/>
</section>

sample.xml

        <tool id="sample" name="Compute correlation">
               <command>java -jar sample.jar</command>
        </tool>

sample.java (exported into a runnable jar file from eclipse)

         package Sample;
         public class Sample 
         {
         public static void main(String[] args)
         {
          System.out.println("Hello world this is important");
         }
         }

When I run the above, (i.e when I click on execute in the middle pane), nothing gets added to my current history. Since there is no visual output of any sort, I am not able to figure out where the problem lies. 

Any help or pointer is appreciated!
Thanks y'all!
VJ.



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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Re: problem integrating new jar file

James Taylor
>>
>> sample.xml
>>
>>         <tool id="sample" name="Compute correlation">
>>                <command>java -jar sample.jar</command>
>>         </tool>


Your tool config does not define any output elements, so no dataset is
created. You need to define at least one output, and then use it's
name in the command line.
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: problem integrating new jar file

Jeremy Goecks
In reply to this post by vijayalakshmi
You'll need to (a) add an output file to your tool configuration ( see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set ) and (b) write your output to the file. See other tool wrappers (e.g. /tools/filters/cutWrapper.xml) for an example.

Good luck,
J.

On Jun 14, 2013, at 1:07 PM, vijayalakshmi wrote:

Hi,

   I am trying to integrate a tool that is written in java into galaxy. The following is what I've done.

1) Created a directory inside /tools directory and put my xml and runnable jar file in it.
2) Linked the xml file in 'tool_conf.xml'.

tool_conf.xml

        <section name="sample tool" id="sample_tool">
<tool file="Sample/sample.xml"/>
</section>

sample.xml

        <tool id="sample" name="Compute correlation">
               <command>java -jar sample.jar</command>
        </tool>

sample.java (exported into a runnable jar file from eclipse)

         package Sample;
         public class Sample 
         {
         public static void main(String[] args)
         {
          System.out.println("Hello world this is important");
         }
         }

When I run the above, (i.e when I click on execute in the middle pane), nothing gets added to my current history. Since there is no visual output of any sort, I am not able to figure out where the problem lies. 

Any help or pointer is appreciated!
Thanks y'all!
VJ.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/