Re: [galaxy-dev] R scripts for DESeq

2012-04-02 Thread 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 vipin...@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.borr...@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...@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 g...@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...@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-...@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 liusongyang2...@gmail.com
   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

Re: [galaxy-dev] R scripts for DESeq

2012-03-26 Thread 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 carlos.borr...@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...@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 g...@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...@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-...@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 liusongyang2...@gmail.com
   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

Re: [galaxy-dev] R scripts for DESeq

2012-03-26 Thread 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 vipin...@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.borr...@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...@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 g...@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...@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-...@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 liusongyang2...@gmail.com
   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

Re: [galaxy-dev] R scripts for DESeq

2012-02-24 Thread Liusong Yang 
Just set up the email alert. Thanks. Lisa

On Wed, Feb 22, 2012 at 9:27 PM, Greg Von Kuster g...@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...@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-...@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 liusongyang2...@gmail.com
 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/

Re: [galaxy-dev] R scripts for DESeq

2012-02-23 Thread 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 g...@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...@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-...@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 liusongyang2...@gmail.com
 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 this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] R scripts for DESeq

2012-02-23 Thread 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 g...@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...@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-...@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 liusongyang2...@gmail.com
  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
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[galaxy-dev] R scripts for DESeq

2012-02-22 Thread Jennifer Jackson 

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 liusongyang2...@gmail.com
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
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Re: [galaxy-dev] R scripts for DESeq

2012-02-22 Thread 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.

inline: email_alert.tiff



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...@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-...@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 liusongyang2...@gmail.com
 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
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 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
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 please use the interface at:
 
 http://lists.bx.psu.edu/
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