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. Peter ___________________________________________________________ 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/
