On Tue, Mar 19, 2013 at 5:38 PM, Hakeem Almabrazi <halmabr...@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.


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