Re: [galaxy-user] new cuffdiff with readgroup problem

2013-11-19 Thread Johanna Sandgren 
Hi Jen,

I know read_group_tracking files are included now as I say in my e-mail below 
(before 11 output files now 15 from your cuffdiff) but the question was if also 
the count_tracking and/or read_group.info files are needed for plotting 
replicate data in CummeRbund, since I do not succeed with the current output. 
So now there is no difference what you can do (at least in CummeRbund) with the 
output compared to when it was 11 output files...? Even though you can choose 
include Read Group Dataset as I do.

Thanks,
Johanna


From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, November 15, 2013 10:23 PM
To: Johanna Sandgren
Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks
Subject: Re: [galaxy-user] new cuffdiff with readgroup problem

Hi Johanna,

Update: I had this incorrect, the option to include Read Group files in the 
output is now available and near the bottom on the Cuffdiff tool form input 
option. Count tracking files are still in the list of open to-do items.

Big thanks to Jeremy for the update!

Jen
Galaxy team
On 11/14/13 2:05 PM, Jennifer Jackson wrote:
Hi Johanna,

Adding in the read_groups and other select output files is a planned 
enhancement for a future date. The Trello ticket to follow progress is here:
https://trello.com/c/lIdpOZ88
related to : https://trello.com/c/U7nceKdj

Good question!

Jen
Galaxy team


On 11/12/13 12:26 AM, Johanna Sandgren wrote:
Hello,

Thanks for your answer. I can see that compared to the output from cuffdiff 
according to their manual (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) 
there are still files missing from galaxy's output. Like the count tracking 
files and read_groups.info. So these are vital for replicate plotting in 
CummeRbund then? When will you also include them in your output?

Regards,
Johanna

From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, October 31, 2013 4:09 AM
To: Johanna Sandgren
Cc: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu; Jeremy 
Goecks
Subject: Re: [galaxy-user] new cuffdiff with readgroup problem

Hello Johanna,

Last time I checked, this specific functionality was not fully implemented yet. 
I do not believe that a firm timeline has been set yet for completion.

Jeremy can comment if I have this incorrect, but I wanted to get back to you so 
that you were not wondering!

Take care,

Jen
Galaxy team




On 10/21/13 8:54 AM, Johanna Sandgren wrote:

Hi,

I have tested the new cuffdiff version in galaxy and was very eager to now also 
get the replicate data for each test. Have anyone tried that yet and succeeded 
with replicates in downstream R package CummeRbund? Even though I successfully 
build database with the now 15 output files (including read group tracking), no 
error message, I can not plot anything with replicates=T.
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: near from: syntax error)


Anyone know the problem?

Thanks,
Johanna

..
Johanna Sandgren, PhD
Department of Oncology-Pathology
CCK, Karolinska Institutet
SE-171 76 Stockholm, Sweden
+46-8-517 721 35 (office),
+46-8- 321047(fax), +46-708 388476 (mobile)






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http://galaxyproject.org




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Re: [galaxy-user] new cuffdiff with readgroup problem

2013-11-15 Thread Jennifer Jackson 

Hi Johanna,

Update: I had this incorrect, the option to include Read Group files 
in the output is now available and near the bottom on the Cuffdiff tool 
form input option. Count tracking files are still in the list of open 
to-do items.


Big thanks to Jeremy for the update!

Jen
Galaxy team

On 11/14/13 2:05 PM, Jennifer Jackson wrote:

Hi Johanna,

Adding in the read_groups and other select output files is a planned 
enhancement for a future date. The Trello ticket to follow progress is 
here:

https://trello.com/c/lIdpOZ88
related to : https://trello.com/c/U7nceKdj

Good question!

Jen
Galaxy team

On 11/12/13 12:26 AM, Johanna Sandgren wrote:


Hello,

Thanks for your answer. I can see that compared to the output from 
cuffdiff according to their manual 
(http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) there are still 
files missing from galaxy's output. Like the count tracking files and 
read_groups, info. So these are vital for replicate plotting in 
CummeRbund then? When will you also include them in your output?


Regards,

Johanna

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Thursday, October 31, 2013 4:09 AM
*To:* Johanna Sandgren
*Cc:* galaxy-user@lists.bx.psu.edu; Jeremy Goecks
*Subject:* Re: [galaxy-user] new cuffdiff with readgroup problem

Hello Johanna,

Last time I checked, this specific functionality was not fully 
implemented yet. I do not believe that a firm timeline has been set 
yet for completion.


Jeremy can comment if I have this incorrect, but I wanted to get back 
to you so that you were not wondering!


Take care,

Jen
Galaxy team



On 10/21/13 8:54 AM, Johanna Sandgren wrote:

Hi,

I have tested the new cuffdiff version in galaxy and was very
eager to now also get the replicate data for each test. Have
anyone tried that yet and succeeded with replicates in downstream
R package CummeRbund? Even though I successfully build database
with the now 15 output files (including read group tracking), no
error message, I can not plot anything with replicates=T.

Error in sqliteExecStatement(con, statement, bind.data) :

  RS-DBI driver: (error in statement: near from: syntax error)

Anyone know the problem?

Thanks,

Johanna


..

Johanna Sandgren, PhD

Department of Oncology-Pathology

CCK, Karolinska Institutet

SE-171 76 Stockholm, Sweden

+46-8-517 721 35 (office),

+46-8- 321047(fax), +46-708 388476 (mobile)




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Galaxy analysis and other features on the public server

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please use the interface at:

  


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--
Jennifer Hillman-Jackson
http://galaxyproject.org


--
Jennifer Hillman-Jackson
http://galaxyproject.org


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http://galaxyproject.org

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Re: [galaxy-user] new cuffdiff with readgroup problem

2013-11-14 Thread Jennifer Jackson 

Hi Johanna,

Adding in the read_groups and other select output files is a planned 
enhancement for a future date. The Trello ticket to follow progress is 
here:

https://trello.com/c/lIdpOZ88
related to : https://trello.com/c/U7nceKdj

Good question!

Jen
Galaxy team

On 11/12/13 12:26 AM, Johanna Sandgren wrote:


Hello,

Thanks for your answer. I can see that compared to the output from 
cuffdiff according to their manual 
(http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) there are still 
files missing from galaxy's output. Like the count tracking files and 
read_groups, info. So these are vital for replicate plotting in 
CummeRbund then? When will you also include them in your output?


Regards,

Johanna

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Thursday, October 31, 2013 4:09 AM
*To:* Johanna Sandgren
*Cc:* galaxy-user@lists.bx.psu.edu; Jeremy Goecks
*Subject:* Re: [galaxy-user] new cuffdiff with readgroup problem

Hello Johanna,

Last time I checked, this specific functionality was not fully 
implemented yet. I do not believe that a firm timeline has been set 
yet for completion.


Jeremy can comment if I have this incorrect, but I wanted to get back 
to you so that you were not wondering!


Take care,

Jen
Galaxy team



On 10/21/13 8:54 AM, Johanna Sandgren wrote:

Hi,

I have tested the new cuffdiff version in galaxy and was very
eager to now also get the replicate data for each test. Have
anyone tried that yet and succeeded with replicates in downstream
R package CummeRbund? Even though I successfully build database
with the now 15 output files (including read group tracking), no
error message, I can not plot anything with replicates=T.

Error in sqliteExecStatement(con, statement, bind.data) :

  RS-DBI driver: (error in statement: near from: syntax error)

Anyone know the problem?

Thanks,

Johanna


..

Johanna Sandgren, PhD

Department of Oncology-Pathology

CCK, Karolinska Institutet

SE-171 76 Stockholm, Sweden

+46-8-517 721 35 (office),

+46-8- 321047(fax), +46-708 388476 (mobile)




___

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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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   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/

  


To search Galaxy mailing lists use the unified search at:

  


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--
Jennifer Hillman-Jackson
http://galaxyproject.org


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] new cuffdiff with readgroup problem

2013-11-12 Thread Johanna Sandgren 
Hello,

Thanks for your answer. I can see that compared to the output from cuffdiff 
according to their manual (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) 
there are still files missing from galaxy's output. Like the count tracking 
files and read_groups, info. So these are vital for replicate plotting in 
CummeRbund then? When will you also include them in your output?

Regards,
Johanna

From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, October 31, 2013 4:09 AM
To: Johanna Sandgren
Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks
Subject: Re: [galaxy-user] new cuffdiff with readgroup problem

Hello Johanna,

Last time I checked, this specific functionality was not fully implemented yet. 
I do not believe that a firm timeline has been set yet for completion.

Jeremy can comment if I have this incorrect, but I wanted to get back to you so 
that you were not wondering!

Take care,

Jen
Galaxy team



On 10/21/13 8:54 AM, Johanna Sandgren wrote:

Hi,

I have tested the new cuffdiff version in galaxy and was very eager to now also 
get the replicate data for each test. Have anyone tried that yet and succeeded 
with replicates in downstream R package CummeRbund? Even though I successfully 
build database with the now 15 output files (including read group tracking), no 
error message, I can not plot anything with replicates=T.
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: near from: syntax error)


Anyone know the problem?

Thanks,
Johanna

..
Johanna Sandgren, PhD
Department of Oncology-Pathology
CCK, Karolinska Institutet
SE-171 76 Stockholm, Sweden
+46-8-517 721 35 (office),
+46-8- 321047(fax), +46-708 388476 (mobile)





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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:



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please use the interface at:



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--

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http://galaxyproject.org
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Re: [galaxy-user] new cuffdiff with readgroup problem

2013-10-30 Thread Jennifer Jackson 

Hello Johanna,

Last time I checked, this specific functionality was not fully 
implemented yet. I do not believe that a firm timeline has been set yet 
for completion.


Jeremy can comment if I have this incorrect, but I wanted to get back to 
you so that you were not wondering!


Take care,

Jen
Galaxy team


On 10/21/13 8:54 AM, Johanna Sandgren wrote:


Hi,

I have tested the new cuffdiff version in galaxy and was very eager to 
now also get the replicate data for each test. Have anyone tried that 
yet and succeeded with replicates in downstream R package CummeRbund? 
Even though I successfully build database with the now 15 output files 
(including read group tracking), no error message, I can not plot 
anything with replicates=T.


Error in sqliteExecStatement(con, statement, bind.data) :

  RS-DBI driver: (error in statement: near from: syntax error)

Anyone know the problem?

Thanks,

Johanna

..

Johanna Sandgren, PhD

Department of Oncology-Pathology

CCK, Karolinska Institutet

SE-171 76 Stockholm, Sweden

+46-8-517 721 35 (office),

+46-8- 321047(fax), +46-708 388476 (mobile)



___
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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
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[galaxy-user] new cuffdiff with readgroup problem

2013-10-21 Thread Johanna Sandgren 

Hi,

I have tested the new cuffdiff version in galaxy and was very eager to now also 
get the replicate data for each test. Have anyone tried that yet and succeeded 
with replicates in downstream R package CummeRbund? Even though I successfully 
build database with the now 15 output files (including read group tracking), no 
error message, I can not plot anything with replicates=T.
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: near from: syntax error)


Anyone know the problem?

Thanks,
Johanna

..
Johanna Sandgren, PhD
Department of Oncology-Pathology
CCK, Karolinska Institutet
SE-171 76 Stockholm, Sweden
+46-8-517 721 35 (office),
+46-8- 321047(fax), +46-708 388476 (mobile)

___
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at usegalaxy.org.  Please keep all replies on the list by
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