Re: [galaxy-user] Is there web-based CummeRbund?

[Carlos Borroto]

Hi Jianguang,

I'm the author of cummeRbund wrapper in the test Galaxy Tool Shed. I
never got around to quite finish it, that's why I never submitted to
main. Also cummeRbund received a big update since the time I was
writing this wrapper. I don't think I can recommend using the wrapper
in its current state at all.

In any case, even if the wrapper could help you, you would need to
deploy a local or a cloud instance of Galaxy,  as is not clear to me
that this wrapper would make its way to Galaxy Main server any time
soon. You would probably be better of by dealing with R and
cummeRbund, which by the way you should be able to use in Windows.

If I find the time to play with the cummeRbund Galaxy wrapper again,
I'll make sure to comment about it in this list.

Best,
Carlos

On Sat, Aug 25, 2012 at 8:09 PM, Dave Clements
 wrote:
> Hi Jianguang,
>
> I went to http://galaxy.psu.edu/search/web/ and searched for cummerbund.
>
> It looks like there is a cummerbund wrapper in the test Galaxy Tool Shed,
> but that is about it.
>
> Dave C
>
> On Fri, Aug 24, 2012 at 3:23 PM, Du, Jianguang  wrote:
>>
>> Dear All,
>>
>> I am going to visualize Cuffdiff outputs. I understand that CummeRbund can
>> be used to visualize Cuffdiff outputs. However, I am not good at Linux
>> system and feel difficult to understand CummeRbund manual. Is there
>> web-based CummeRbund program (like Tophat and Cufflink) available for use?
>>
>> If web-based CummeRbund does not exist, is there other web-based program
>> can be used to visualize Cuffdiff outputs?
>>
>> Thanks.
>>
>> Jianguang
>>
>>
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>>
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>>
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>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>
>
>
>
> --
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>
>
> ___
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> use the Galaxy Development list:
>
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>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
___
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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] Is there web-based CummeRbund?

[Dave Clements]

Hi Jianguang,

I went to http://galaxy.psu.edu/search/web/ and searched for cummerbund.

It looks like there is a cummerbund wrapper in the test Galaxy Tool Shed,
but that is about it.

Dave C

On Fri, Aug 24, 2012 at 3:23 PM, Du, Jianguang  wrote:

>  Dear All,
>
> I am going to visualize Cuffdiff outputs. I understand that CummeRbund can
> be used to visualize Cuffdiff outputs. However, I am not good at Linux
> system and feel difficult to understand CummeRbund manual. Is there
> web-based CummeRbund program (like Tophat and Cufflink) available for use?
>
> If web-based CummeRbund does not exist, is there other web-based program
> can be used to visualize Cuffdiff outputs?
>
> Thanks.
>
> Jianguang
>
> ___
> 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/
>



-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
___
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:

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[galaxy-user] Is there web-based CummeRbund?

[Du, Jianguang]

Dear All,

I am going to visualize Cuffdiff outputs. I understand that CummeRbund can be 
used to visualize Cuffdiff outputs. However, I am not good at Linux system and 
feel difficult to understand CummeRbund manual. Is there web-based CummeRbund 
program (like Tophat and Cufflink) available for use?

If web-based CummeRbund does not exist, is there other web-based program can be 
used to visualize Cuffdiff outputs?

Thanks.

Jianguang
___
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/