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-cloud_...

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/

---

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/

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/

---

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/

The University of Dundee is a registered Scottish Charity, No: SC015096

---

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/

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/

---

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/

The University of Dundee is a registered Scottish Charity, No: SC015096

---

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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Hello Vipin,

Good to see this. just a quick question, does your interface has the functionality to define groups (say normal or control) for replicates/samples, as the way we define in edgeR/DESeq R script.

Carlos, I think BAM input would be okay as it can be connected with tophat in the workflow.

Let me know your suggestions.

Praveen.

-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Carlos Borroto Sent: Tuesday, March 27, 2012 12:44 AM To: Vipin TS Cc: Galaxy Dev Subject: Re: [galaxy-dev] R scripts for DESeq

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/ > >

---

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:

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---

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:

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The University of Dundee is a registered Scottish Charity, No: SC015096

---

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:

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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_threadhttp://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%20Listshttp://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-devhttp://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/