Read simulator

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Read simulator

garzetti
Dear all,

I would like to perforn my SNP calling pipeline (for MySeq Illumina
reads) to previously sequenced and assembled genomes.
Is there any read simulator in the Main Galaxy?
I am looking for something like the wgsim algorithm in SAMtools...

Thanks!
Debora
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Re: Read simulator

Jen Hillman-Jackson
Hi Debora,

There isn't a tool to do this on the public Main Galaxy server at
http://usegalaxy.org. But I did just create a ticket to have a wrapped
tool in the Tool Shed added to Main for this function. You can "up-vote"
to help it become prioritized, and also comment if you have a preference
between the choices listed in the description or want to suggest an
alternate:
https://trello.com/c/z0MLCQHU
https://wiki.galaxyproject.org/Issues

The Tool Shed's repository "wgsim" could likely be run in a local Galaxy
with modest resources without too much trouble. If you want to try, this
is how to get started. The repository "grinder" I believe is more
compute intensive, but you could test this. Moving to a cloud would work
for both.
http://getgalaxy.org
http://usegalaxy.org/toolshed
http://usegalaxy.org/cloud

And, one final option is to locate a public Galaxy server that hosts a
tool for this function. I don't know of one off hand, but the list of
servers is here:
https://wiki.galaxyproject.org/PublicGalaxyServers

Thanks!

Jen
Galaxy team



On 2/20/14 4:30 AM, garzetti wrote:

> Dear all,
>
> I would like to perforn my SNP calling pipeline (for MySeq Illumina
> reads) to previously sequenced and assembled genomes.
> Is there any read simulator in the Main Galaxy?
> I am looking for something like the wgsim algorithm in SAMtools...
>
> Thanks!
> Debora
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>
>  http://galaxyproject.org/search/mailinglists/

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

___________________________________________________________
The Galaxy User list should be used for the discussion of
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Re: Read simulator

Xianrong Wong
In reply to this post by garzetti
Hi, I've been trying to use the extra DNA tool but I keep getting an error:

Traceback (most recent call last): File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 300, in if __name__ == "__main__": __main__() File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 113, in __main__

I tried it on a dataset which worked 2 days ago but it is failing now too.

Jose

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Re: Read simulator

Jen Hillman-Jackson
Hello Jose,

We are investigating other similar related problems. Would you please submit the problem as a bug report if you have not already done so and we will follow up with you there. Also, please try to ask questions by starting a new thread (brand new message, new subject line). Do not use "reply" to existing Q & A thread on the mailing list. This helps us with tracking.

Best,

Jen
Galaxy team

On 2/21/14 11:14 AM, Xianrong Wong wrote:
Hi, I've been trying to use the extra DNA tool but I keep getting an error:

Traceback (most recent call last): File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 300, in if __name__ == "__main__": __main__() File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 113, in __main__

I tried it on a dataset which worked 2 days ago but it is failing now too.

Jose


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

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

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

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Jennifer Hillman-Jackson
http://galaxyproject.org