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-cloud_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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