I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin 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 /mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin But I always see /bin/sh: bowtie: not found As an error message. How can I get the path set correctly? Brad -- Brad Langhorst New England Biolabs langho...@neb.com
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