Errors With Apt-Get When Attempting To Install Somaticsniper

Question

[N]

Hi!

I'm trying to get SomaticSniper to run on Ubuntu 10.04 and I've been following the instruction from the website below:

http://gmt.genome.wustl.edu/somatic-sniper/1.0.2/install.html

However, when I run the command:

sudo apt-get update

I encounter three errors (at the end of the post) along with several successfull hits. Looks like the address http://repo.gsc.wustl.edu is not accessible. I would be greatfull for advise on how to make the installation work.

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W: Failed to fetch http://repo.gsc.wustl.edu/ubuntu/dists/lucid-genome-development/Release.gpg Something wicked happened resolving 'repo.gsc.wustl.edu:http' (-5 - No address associated with hostname)

W: Failed to fetch http://repo.gsc.wustl.edu/ubuntu/dists/lucid-genome-development/main/binary-i386/Packages.gz Something wicked happened resolving 'repo.gsc.wustl.edu:http' (-5 - No address associated with hostname)

W: Failed to fetch http://repo.gsc.wustl.edu/ubuntu/dists/lucid-genome-development/main/i18n/Translation-en_US.bz2 Something wicked happened resolving 'repo.gsc.wustl.edu:http' (-5 - No address associated with hostname)

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[fo3c]

I would think it's a problem on your end. Ubuntu forums might help.

[lh3]

You are right that repo.gsc.wustl.edu is offline. Then the only option is to build from the source code following the github instruction. I used to compile it a few months ago.

[Daniel]

It's times like this that I value the existence of http://www.downforeveryoneorjustme.com/

[nnutter]

"Only option" is a bit extreme. ;-)

[lh3]

Yeah, you are right. I should not say that.

Answer 1

[nnutter]

repo.gsc.wustl.edu is our internal, private APT repo. You should be using apt.genome.wustl.edu. Where did you see repo.gsc.wustl.edu? I'd like to fix the issue.

Edit: It looks like our install.sh is misconfigured to point to our repo.gsc.wustl.edu instead of apt.genome.wustl.edu. We'll work on getting that fixed but in the mean time you can edit /etc/apt/sources.list.d/genome.list to correct the address. After editing do an apt-get update to refresh your APT caches.

Edit: install.sh has been fixed and deployed.

Answer 2

[N]

Thanks! The previous errors are gone now. Unfortunately there's a new one. This time the address is available, seems to be a problem with the signature verification.

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W: A error occurred during the signature verification. The repository is not updated and the previous index files will be used.GPG error: https://apt.genome.wustl.edu lucid-genome Release: Unknown error executing gpgv

W: Failed to fetch https://apt.genome.wustl.edu/ubuntu/dists/lucid-genome/Release

W: Some index files failed to download, they have been ignored, or old ones used instead.