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.
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)
2 answers
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.
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.
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.
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I would think it's a problem on your end. Ubuntu forums might help.
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.
It's times like this that I value the existence of http://www.downforeveryoneorjustme.com/
"Only option" is a bit extreme. ;-)
Yeah, you are right. I should not say that.