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Old 09-07-2011, 06:16 AM   #4
arolfe
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Location: 02119

Join Date: Jul 2011
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You have at least two options:

1) figure out what dotfiles are being used when your job is executed and modify those. I'd save this for the next time you're bored.

2) set PATH in your job. You could do this by
a) writing a script that sets PATH and then invokes tophat
b) qsub "PATH=${PATH}:/path/to/bowtie tophat ....."

Note that the behavior of (b) depends on whether you use single or double quotes. Double will use PATH from the shell where you call qsub. Single will use PATH from inside the job.
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