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Question: Tophat2 on Cloudman Stuck 'Cloning'
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gravatar for madkisson
3.7 years ago by
madkisson • 30
United States
madkisson • 30 wrote:

Hi

Total newbie here. I've spent the last 4 days getting Cloudman to work [issues with Amazon] only to find that I can't get access to Tophat2 [which is a fairly key component to what i want to do]. I've tried installing it from the Toolshed but I get this message: 'Initializing repository installation failed', and then it hangs in 'cloning' state for almost 24 hours now [with a couple of uninstall/reinstalls in there]. What am I doing wrong?

Thanks

Michael
rna-seq tophat cloud galaxy • 1.0k views
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modified 3.7 years ago by Enis Afgan • 690 • written 3.7 years ago by madkisson • 30

 Cloning...

ADD REPLY • link written 3.7 years ago by madkisson • 30
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gravatar for Enis Afgan
3.7 years ago by
Enis Afgan • 690
United States
Enis Afgan • 690 wrote:

It looks like this is due to the version of Galaxy running on the cloud, which is a bit dated at this point. We are preparing a new release that should be out soon.

In the mean time, you can update the version of Galaxy running on your cloud instance. This can be done from CloudMan's Admin page by clicking on 'Update Galaxy' button and waiting several minutes until everything gets updated.

Note that this version of Galaxy only has a few genomes indexed for use by Tophat2 (mm10, hg19 and GRCh37) so you may need to add more genomes. Data Managers can be used to help there: https://wiki.galaxyproject.org/Admin/Tools/DataManagers

The upcoming cloud version will have more of this available out of the box. Sorry for the trouble and let us know if you have more questions.
ADD COMMENT • link written 3.7 years ago by Enis Afgan • 690

THANK YOU! This explains so much - I thought things would be easier on Cloudman over the public version but it's been far more difficult. Looking forward to the new release. Updating my version now. Thanks for the help. Fortunately all of my data has been processed using Mouse mm10, so I'm good once galaxy is updated

ADD REPLY • link written 3.7 years ago by madkisson • 30

It worked! Thanks again!

ADD REPLY • link written 3.7 years ago by madkisson • 30
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