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Question: Aachanges
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gravatar for David Joly
7.3 years ago by
David Joly • 100
David Joly • 100 wrote:
Hi everybody, Maybe a dumb question but does someone know if we can use the aaChanges tool on a custom genome? I have my SNP dataset and my gene dataset but I can only assign them to one of the genome build already in UCSC... I am using the web server of galaxy. Do I need to install my own local instance of Galaxy in order to add a custom genome build? Thanks, David
galaxy • 879 views
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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by David Joly • 100
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
===> Please use "Reply All" when responding to this email!<=== Hello David, You are correct, this tool will only function when a database is defined with Galaxy already. This will include databases from UCSC and other sources and it sounds like you have already checked using the "Edit Attributes" form (pencil icon). Using a custom genome currently would require a local instance where you could add you own genomes to the list of available databases. http://getgalaxy.org This may be a requirement that could be changed (ability to leave database as unassigned). I opened a request ticket that you can follow to see the review result for this proposal: https://bitbucket.org/galaxy/galaxy-central/issue/649/modify- aachanges-tool-to-allow-undefined Thanks for sending in the suggestion! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
Thanks! I decided to install a local instance of Galaxy. The installation went fine, but now I'm not sure how to add a custom genome. I found some information in past comments on the user list but I'm not sure I understand everything. All I've got is a fasta file with all my supercontigs and a gtf file with the predicted models. And a somewhat basic question: am I supposed to be able to log in a local instance? It doesn't recognize my username and password, which I guess is normal since it is local, so what should I do? Cheers, David 2011/8/26 Jennifer Jackson <jen@bx.psu.edu>
ADD REPLY • link written 7.3 years ago by David Joly • 100
Hello David, The main hub for administration tasks is: http://galaxyproject.org/Admin To set up data, please see "Data Integration" and "NGS Local Setup". If this is just your own local instance, you may not need to follow all of the procedures. And you are correct, any log in would be specific to your instance. Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD REPLY • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
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