Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so
that he or or one of the developers more experienced with
troubleshooting cloud issues can help. My guess is that there is a path
problem (covered in the first wiki link) but by no means is that the
only possibility.
Thanks!
Jen
Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local
galaxy install. I am using the cloudman from aws and it seemed to have
everything for having the input files and reference genome chose. The
job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
**
*From:*Jennifer Jackson [mailto:[email protected]]
*Sent:* Friday, January 11, 2013 3:48 AM
*To:* Sun, Wenping [USA]
*Cc:* [email protected]
*Subject:* [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the
actual MACS tool and set up the proper configuration paths? Details
for how to do this are in these wikis:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS,
groomed fastq datasets first need to be mapped. An example can be
found in our Using Galaxy paper, protocol #3. Links to the paper and
supplemental materials (including a screencast walk-through) are
available here:
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to
the [email protected] <mailto:[email protected]> mailing list
would be best,
Thanks!
Jen
Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I've encountered the error while running macs on galaxy for
chipseq data. I used fastq groomed files as input and had the
following error
An error occurred running this job: //bin/sh: macs: not found/
//
Anybody can kindly provide some hints?
Thanks,
Kathryn
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Jennifer Hillman-Jackson
Galaxy Support and Training
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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