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:jen@bx.psu.edu]
Sent: Friday, January 11, 2013 3:48 AM
To: Sun, Wenping [USA]
Cc: galaxy-user@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-dev@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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