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] < lynny@mail.nih.gov> 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. lynny@mail.nih.govmailto: lynny@mail.nih.gov | http://twitter.com/bioinformatics1

Stay connected with the NIH Library NIH Library: http://nihlibrary.nih.govhttp://nihlibrary.nih.gov/ | Facebook: http://www.facebook.com/nihlibrary | Twitter: http://www.twitter.com/nihlibhttp://www.twitter.com/nihlib _____________________________ Amazing Research. Amazing Help.

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I believe subsequent jobs should use the new paths automatically, yes.

On Mon, Nov 18, 2013 at 12:14 PM, Young, Lynn (NIH/OD/ORS) [E] < lynny@mail.nih.gov> wrote:

Hi Dannon,

I edited the file.

Will the system automatically recognize the change?

Warmly, Lynn

From: Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com> Date: Monday, November 18, 2013 1:06 PM To: Lynn Young <lynny@mail.nih.govmailto:lynny@mail.nih.gov> Cc: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" < galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November

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] < lynny@mail.nih.govmailto:lynny@mail.nih.gov> 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. lynny@mail.nih.govmailto: lynny@mail.nih.gov<mailto:lynny@mail.nih.govmailto:lynny@mail.nih.gov> | http://twitter.com/bioinformatics1

Stay connected with the NIH Library NIH Library: http://nihlibrary.nih.govhttp://nihlibrary.nih.gov/ | Facebook: http://www.facebook.com/nihlibrary | Twitter: http://www.twitter.com/nihlibhttp://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/