This may be due to an incorrect reference to '/mnt/galaxyTools' in the galaxy user's .sge_request file.
If you're comfortable with ssh and editing files on the server, you can log in and edit the file (the path should be /mnt/galaxy instead), and you should be good to go. Feel free to reply offline if you're not comfortable with this and would like me to take a look directly. On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] < [email protected]> wrote: > Hi, > > We're using Galaxy Cloud -> New Cloud Cluster to create instances of > Galaxy for training on Wednesday 20 November. > > When we try to view a bam file using Trackster, we get the following error: > > > /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: > bedtools: command not found > /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: > bedGraphToBigWig: command not found > > Please let us know how to proceed. > > Sincerely, > > Lynn > > Lynn Young, PhD | Informationist/Bioinformatics Scientist | National > Institutes of Health Library | Office of Research Services | Building 10, > Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T. > 301-594-6426 | F. 301-402-0254 | E. [email protected]<mailto: > [email protected]> | http://twitter.com/bioinformatics1 > > Stay connected with the NIH Library > NIH Library: http://nihlibrary.nih.gov<http://nihlibrary.nih.gov/> | > Facebook: http://www.facebook.com/nihlibrary | Twitter: > http://www.twitter.com/nihlib<http://www.twitter.com/nihlib> > _____________________________ > Amazing Research. Amazing Help. > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
