Re: [galaxy-dev] R scripts for DESeq

[Vipin TS]

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-...@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
>>
>> 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 
>> To: galaxy-u...@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/

Re: [galaxy-dev] R scripts for DESeq

[Praveen Raj Somarajan]

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-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@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  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  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  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"  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 
>> >> >> 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-...@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_threa

Re: [galaxy-dev] R scripts for DESeq

[Carlos Borroto]

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  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  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  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"  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 
>> >> >> 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-...@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
>> >>
>> >> >
>> >> > > >> >> >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 
>> >>  To: galaxy-u...@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 

Re: [galaxy-dev] R scripts for DESeq

[Vipin TS]

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  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  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"  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 
> 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-...@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 
> >>  To: galaxy-u...@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

Re: [galaxy-dev] R scripts for DESeq

[Carlos Borroto]

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  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"  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  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-...@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
>>
>> > >> >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 
>>  To: galaxy-u...@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/
>> >>
>> >
>> >
>> >
>> >___

Re: [galaxy-dev] R scripts for DESeq

[Liusong Yang]

Just set up the email alert. Thanks. Lisa

On Wed, Feb 22, 2012 at 9:27 PM, Greg Von Kuster  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  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-...@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 
 To: galaxy-u...@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/
>>
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Re: [galaxy-dev] R scripts for DESeq

[Vipin TS]

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"  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  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-...@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 
>  To: galaxy-u...@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

Re: [galaxy-dev] R scripts for DESeq

[Christian Cole]

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"  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  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-...@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
>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 
 To: galaxy-u...@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


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Re: [galaxy-dev] R scripts for DESeq

[Greg Von Kuster]

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  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-...@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 
>>> To: galaxy-u...@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/
> 

___
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and other Galaxy lists, please use the interface at:

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Re: [galaxy-dev] R scripts for DESeq

[Liusong Yang]

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  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-...@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 
>> To: galaxy-u...@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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Re: [galaxy-dev] R scripts for DESeq

[Vipin TS]

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-...@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
>
> 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 
> To: galaxy-u...@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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