10 Aug
2009
10 Aug
'09
10:20 a.m.
Nate Coraor wrote:
Thanks for the clarification.
However, for my non-interpretor tools Galaxy seems to be ignoring my $PATH (set in ~/.bash_profile). My jobs run on the cluster via SGE so is this likely to be a Galaxy issue or SGE?
Chances are it's SGE. You may want to double check what $PATH is in SGE by running a few test jobs.
Just realised I only replied to Nate. Reposted below: It was. In looking for a solution the very handy $HOME/.sge_request file came to the rescue. I can now have specific SGE settings for just the galaxy user on our cluster (including the $PATH). Cheers, CHris