This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks!
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh quang.trinh@gmail.com wrote:
Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at
https://github.com/modENCODE-DCC/Galaxy
Please give it a try and send us your comments/questions to help@modencode.org.
Thanks,
Q
On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson jen@bx.psu.edu wrote:
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 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
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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