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.tr...@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
> h...@modencode.org.
>
> Thanks,
>
> Q
>
> On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson <j...@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: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 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
>>
>>
>> --
>> 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:
>>
>>   http://lists.bx.psu.edu/
>
> ___________________________________________________________
> 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:
>
>   http://lists.bx.psu.edu/

___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to