Question: Add table_annovar.pl to PATH : How/where ?
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gravatar for christophe.habib
21 months ago by
France
christophe.habib340 wrote:

Hello everyone,

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.

Thank you,

Christ

ADD COMMENTlink written 21 months ago by christophe.habib340

Well, in this configuration you must add annovar to path with "environment_setup_file" in the galaxy.ini... Be careful if you put this file in config, you need to make "config/path.txt".

ADD REPLYlink written 21 months ago by christophe.habib340
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