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Question: Tophat
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gravatar for giovanni stefani
8.2 years ago by
giovanni stefani • 30
giovanni stefani • 30 wrote:
Hello, I am a new galaxy user, still trying to find my way around. Is there a way to run Tophat on Galaxy? Thanks Giovanni
galaxy • 735 views
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modified 7.8 years ago by Jeremy Goecks • 2.2k • written 8.2 years ago by giovanni stefani • 30
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gravatar for Jeremy Goecks
8.2 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Hi Giovanni, Tophat is available on our test server ( http://test.g2.bx.psu.edu/ ), and it will be available on our main server soon. FYI, our test server can be somewhat unreliable, but you're welcome to try your Tophat analyses there. Thanks, J.
ADD COMMENT • link written 8.2 years ago by Jeremy Goecks • 2.2k
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8.2 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
[cc'ing galaxy-user] Test and Main do not share databases, so you'll need to create an account on Test and (re)upload your data to Test as well. However, here's a trick for moving datasets between Galaxy servers: use the 'save' link next to a dataset (the link for the 'disk' icon) as the URL for a dataset that you want to 'upload.' This will enable you to quickly move datasets between Galaxy servers without having to upload again from your computer. Also, we're working on functionality that will make it easier to move Galaxy histories between servers, but it's not quite ready yet. Best, J. J.
ADD COMMENT • link written 8.2 years ago by Jeremy Goecks • 2.2k
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7.8 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Ying, Unfortunately, your job is too large for our cluster. Our cluster has a limit of 250GB of disk space, and Tophat is exceeding this limit while running your job (Tophat generates many intermediary files when running, including a very large SAM file). Your best bet is to set up and use our cloud instance ( https://bitbucket.org/galaxy/galaxy-central/wiki/cloud ); otherwise, if you have enough resources locally, you can set up a local instance ( https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy ) . Thanks, J.
ADD COMMENT • link written 7.8 years ago by Jeremy Goecks • 2.2k
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