Update custom package URLs and versions

[rchekaluk]

This primarily updates a few failing download urls:

• abyss
• hydra
• MOSAIK
• trinity

However, it also takes the opportunity to update versions to current. Furthermore, some of the previous versions fail to compile under Ubuntu xenial. The following package versions are updated:

• abyss
• boost
• MOSAIK
• trinity
• velvet

[chapmanb]

Thanks for all the fixes and updates. As an FYI we've primarily moved over to using bioconda for package installation instead of these custom scripts:

https://bioconda.github.io/
https://github.com/bioconda/bioconda-recipes

and standard uses of cloudbiolinux, like bcbio installation, use these conda packages:

https://github.com/chapmanb/cloudbiolinux/tree/master/contrib/flavor/ngs_pipeline_minimal

That might be a more useful place to start to get up to date packages. Hope this helps and thank you again.

[rchekaluk]

OK, but heads-up that this PR fixes build issues that occur when simply running the basic CloudBioLinux build as documented:
fab -f fabfile.py -H localhost install_biolinux

If CloudBioLinux is still intended to be used standalone, it sounds to me like it needs to be updated to retire "custom scripts" and supplant them with bioconda.

[chapmanb]

Thanks much for the feedback. Our intention has been to try and work from custom recipes rather than the all in one CloudBioLinux approach, since the number of packages are getting too high. Since we use this for bcbio this is the recommended way to get started:

https://github.com/chapmanb/cloudbiolinux#quick-start

Would that work for what you need or do you require additional packages not present in this recipe?