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: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 mailto: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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
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