On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS <
vipin.ts@gmail.com> wrote:
> Hi Chris,
>
> We are running DESEQ_VERSION 1.6.0 at our instance
>
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
>
> thanks,
> --Vipin T S
>
>
>
>> Which version of DESeq does this tool use?
>>
>> Note that there are significant differences between DESeq 1.4 (the version
>> described in the paper) and 1.6.x (current release). The differences are
>> both in functionality and results.
>> Regards,
>>
>>
>> Chris
>>
>> On 23/02/2012 02:27, "Greg Von Kuster" <
greg@bx.psu.edu> wrote:
>>
>> >Lisa,
>> >
>> >In case you aren't aware, you can set your user preferences for your
>> >account in the tool shed to receive an email message when a new
>> >repository's first upload occurs. This would keep you from having to
>> >check the tool shed. Go to User -> Preferences -> Manage
>> > your email alerts and you'll see the following setting.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
>> >
>> >> Hi Vipin,
>> >> That is a wonderful news and I am eager to see it in tool shed. I am
>> >> going to check tool shed frequently these days to get it asap.
>> >>
>> >> Thanks
>> >> Lisa
>> >>
>> >> On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <
vipin.ts@gmail.com> wrote:
>> >>> Hi,
>> >>>
>> >>> We have the recent release version of DESeq at our Galaxy instance,
>> >>>
>> >>>
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
>> >>>
>> >>> I will add the Galaxy wrapper for DESeq in community tool shed in few
>> >>>days.
>> >>>
>> >>> regards,
>> >>> --Vipin
>> >>>
>> >>>> Hi Lisa,
>> >>>>
>> >>>> I am going to send your question over to the
galaxy-dev@bx.psu.edu
>> >>>>mailing
>> >>>> list so that the development community can offer feedback.
>> >>>>
>> >>>>
>>
>> > >
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
>> >d_instance.2C_or_development_thread
>>
>> > ><
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
>> >ud_instance.2C_or_development_thread>
>> >>>>
>> >>>> Th galaxy-user list is primarily for tool/data usage on the Galaxy
>> >>>>public
>> >>>> server.
>> >>>>
http://wiki.g2.bx.psu.edu/Mailing%20Lists
>> >>>>
>> >>>> Thanks,
>> >>>>
>> >>>> Jen
>> >>>> Galaxy team
>> >>>>
>> >>>>
>> >>>> -------- Original Message --------
>> >>>> Subject: [galaxy-user] R scripts for DESeq
>> >>>> Date: Tue, 21 Feb 2012 23:25:35 -0500
>> >>>> From: Liusong Yang <
liusongyang2009@gmail.com>
>> >>>> To:
galaxy-user@lists.bx.psu.edu
>> >>>>
>> >>>> Hello,
>> >>>>
>> >>>> I am planning to put DESeq into galaxy. I am a newcomer for both
>> >>>> Galaxy and R. I have already read all of the related discussion in
>> >>>> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
>> >>>> added into galaxy recently under the path of tools.
>> >>>>
>> >>>> These lines are from r_wrapper.sh.
>> >>>>
>> >>>> ### Run R providing the R script in $1 as standard input and passing
>> >>>> ### the remaining arguments on the command line
>> >>>>
>> >>>>
>> >>>> I guess this means we need to give the DESeq R script to the wrapper
>> >>>> as standard input. My question is where or what is the DESeq R
>> >>>> scripts? I installed R and DESeq package, but I can not fund anything
>> >>>> like DESeq.R or something similar? I feel so confusing now. Any
>> >>>> comments or suggestions would be absolutely appreciated!
>> >>>>
>> >>>> Thanks
>> >>>>
>> >>>> Lisa
>> >>>> ___________________________________________________________
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>> >>>
>> >>
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