Question: Tophat in Cloudman: missing built-in genome
0
gravatar for karmella.haynes
21 months ago by
United States
karmella.haynes40 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

ADD COMMENTlink modified 21 months ago by Mo Heydarian790 • written 21 months ago by karmella.haynes40

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

ADD REPLYlink written 21 months ago by Mo Heydarian790

I did not launch it that way. I set up an Amazon Cloud account and launched it via http://###.###.##/cloud/

ADD REPLYlink modified 21 months ago • written 21 months ago by karmella.haynes40

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

ADD REPLYlink written 21 months ago by Mo Heydarian790

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.

ADD REPLYlink written 21 months ago by karmella.haynes40

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.

ADD REPLYlink modified 21 months ago • written 21 months ago by karmella.haynes40
1
gravatar for Mo Heydarian
21 months ago by
Mo Heydarian790
United States
Mo Heydarian790 wrote:

Hi Karmella,

Glad you figured out the problem.

The version numbers you see, 0.9 and 2.1.0, are in reference to the Tophat wrapper version, not the version of Tophat. The two wrappers differ only in the default options for the 'coverage-search' option, but both are using the same (and latest) version of Tophat.

Thanks for using Galaxy!

Cheers,

Mo Heydarian, Galaxy Team

ADD COMMENTlink written 21 months ago by Mo Heydarian790

Thank you! This completely addresses my issue in a very timely manner.

Thank you for offering and supporting Galaxy!

ADD REPLYlink written 21 months ago by karmella.haynes40
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