I managed to have everything I wanted for my local galaxy instance (houra!) : - HTCondor as scheduler - UWSGI web server and 2 handlers - Supervisor to manage them - many tools.
The thing is ANNOVAR can't be found by the thing that is launching the script itself :
/home/galaxy/diag_19102015/galaxy/database/job_working_directory/005/5846/tool_script.sh: 9: /home/galaxy/diag_19102015/galaxy/database/job_working_directory/005/5846/tool_script.sh: table_annovar.pl: not found
So my guess is that PATH env variable is not exported to the thing that launch the script. I managed to solve this problem by making symbolic links of annovar perl scripts in /usr/bin. But this is DIRTY and not satisfying because I still don't understand what didn't work in my configuration. So I have 2 questions :
In this configuration, which thing is really launching the scripts ? I think it is HTCondor, but I didn't find how to add annovar directory to its path... so : How/where should I add annovar directory to PATH to make things work ?
I hope you could help me with this last thing.