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:j...@bx.psu.edu]
*Sent:* Friday, January 11, 2013 3:48 AM
*To:* Sun, Wenping [USA]
*Cc:* galaxy-u...@bx.psu.edu
*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 galaxy-...@bx.psu.edu <mailto:galaxy-...@bx.psu.edu> 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
http://galaxyproject.org

--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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