Thanks for the update.
I wonder if when you had the time to upload your script to the toolshed, you could use a different name from just plain DESeq to avoid confusion. A researcher might expect a DESeq tool to use a read count table and not BAM files as input.
Kind regards, Carlos
On Mon, Mar 26, 2012 at 2:49 PM, Vipin TS vipin.ts@gmail.com wrote:
Hi Carlos, Currently I am in a transition period, and I didn't get much time to look on the same, Sorry for the delay.
For getting the read count, we wrote script and which is wrapped in Deseq main program.
regards, --Vipin T S
On 26 March 2012 14:01, Carlos Borroto carlos.borroto@gmail.com wrote:
Hi Vipin,
I was wondering if there is any progress on getting your DESeq wrapper into the Tool Shed? I'm also highly interested on using DESeq inside Galaxy.
Also, what you use for generating the read counts for DESeq? Do you produce these counts inside Galaxy?
Thanks, Carlos
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 >> ___________________________________________________________ >> 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/ >> ___________________________________________________________ >> >> 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/ > >
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