Galaxy wrapper for DESeq 1.6.0 is now available at Galaxy Tool Shed under statistics. --Vipin
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.edumailing 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<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<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
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