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
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:
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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
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:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
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garzetti -
Jennifer Jackson -
Xianrong Wong