Question: Tophat in Cloudman: missing built-in genome
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karmella.haynes • 40 wrote:
Hell all,
After several days of struggling, I finally managed to set up a Galaxy instance in Cloudman...only to discover that I cannot run Tophat because there are no built-in genomes. I want to use the Human Feb. 2009 hg19 reference data: Human (Homo sapiens) (b37): hg19
I set up a Cloudman instance in order to save time and enable faster processing. Unfortunately I have lost a lot of precious time ahead of a research publication deadline.
I am not a developer or programmer. Can someone please provide simple step-by-step instructions on how get a reference genome installed so that i can run Tophat on my fastq files?
Thank you, ---Karmella
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modified 2.3 years ago
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Mo Heydarian ♦ 830
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2.3 years ago by
karmella.haynes • 40
Hi Karmella,
How did you launch your Cloudman instance? If launching from https://launch.usegalaxy.org/launch you should have many reference genomes pre-loaded for use with Tophat (including hg19).
Cheers, Mo Heydarian, Galaxy Team
I did not launch it that way. I set up an Amazon Cloud account and launched it via http://###.###.##/cloud/
Hi Karmella,
I recommend launching Cloudman from https://launch.usegalaxy.org/launch. From this page you only need to enter your AWS credentials (access and secret keys), specify a password, and increase your storage (if needed), then you should have a Cloudman instance spun up within minutes.
Also, you entered what seems to be your Cloudman address in your previous reply. You may want to edit your post to remove the address.
Cheers, Mo Heydarian, Galaxy Team
Thank you. Now that I remember correctly, I did launch through https://launch.usegalaxy.org/launch, which generated a unique address. Once my Cloudman instance was set up, I logged in with the username I set up for myself (and made myself admin). After following these steps, I have been able to upload and concatenate fastq files, but now I cannot run Tophat because the built-in reference genomes appear to be missing.
Wait, I figured out the problem.
In my Coud, the built-in genomes do appear for Tophat Galaxy Version 0.9.
I recently added Tophat Galaxy Version 2.1.0 in order to be consistent with some previous work I did in the usegalaxy.org environment. In my Cloud, I cannot access built-in genomes through 2.1.0.
Should I be concerned about running Version 0.9 instead of 2.1.0? Will this generate significant differences in my data?
Thank you for your patience.