On Tue, Mar 19, 2013 at 5:38 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:

Hi,

I am sure these questions had been asked before but could not find the right answer or did not look enough J . I just want to add new aligner tool wrapper into local galaxy. I used the existing wrappers (i.e bwa) as template and then modified it accordingly.

Here are what I did:

Create an xml file and put it to “~tools/sr_mapping/mytool.xml”

· Created a py file and added it to the same folder “~tools/sr_mapping/myTool.py”

· Configured the tool_conf.xml file

· Restarted my galaxy server

However, the new tool did not show up in the GUI.

Is there anything else I am missing?

Is there a validation step I need to perform for both files?

I appreciate your help.

First put your XML file though a standard XML validator (there are lots online), which will spot any silly things like broken tags. Second, when you restart Galaxy, I like to do this by running the run.sh script at the terminal so I can see the output on screen. Look for any error message when it loads your tool - this is usually enough to identify the problem. Peter