I have the software for our SGE cluster (eg. Bowtie) in 
And I've set the PATH environment in the galaxy user's .bashrc

export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"

When I  echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job 
runner node

But I always see /bin/sh: bowtie: not found
As an error message.

How can I get the path set correctly?

Brad Langhorst
New England Biolabs

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