dhivya arasappan wrote:
Hi,
We have a local instance of galaxy at our institution. I've been trying to use several existing wrappers for tools on galaxy right now, for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks through galaxy. I keep seeing the following error:
An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found
An error occurred running this job:Could not determine cufflinks version cufflinks -I 300000 -F 0.050000 -j 0.050000 -p 4 -Q 0 -r Error running cufflinks. /bin/sh: cufflinks: not found
This is despite the server having cufflinks and bwa available. Is there somewhere I need to put these executables? Any config/ini files that I need to update with the location of the executables?
Hi Dhivya, If you log in as the user which runs the Galaxy process, is `bwa` available on the $PATH (e.g. on the command line w/o specifying a path). Thanks, --nate
Thanks for any help, Dhivya
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: