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] <
ly...@mail.nih.gov> wrote:

> Hi Dannon,
>
> I edited the file.
>
> Will the system automatically recognize the change?
>
> Warmly,
> Lynn
>
> From: Dannon Baker <dannon.ba...@gmail.com<mailto:dannon.ba...@gmail.com>>
> Date: Monday, November 18, 2013 1:06 PM
> To: Lynn Young <ly...@mail.nih.gov<mailto:ly...@mail.nih.gov>>
> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <
> galaxy-dev@lists.bx.psu.edu<mailto: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] <
> ly...@mail.nih.gov<mailto:ly...@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. ly...@mail.nih.gov<mailto:
> ly...@mail.nih.gov><mailto:ly...@mail.nih.gov<mailto:ly...@mail.nih.gov>>
> | http://twitter.com/bioinformatics1
>
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