search

broadinstitute / viral-ngs-deploy

Deployment files related to https://github.com/broadinstitute/viral-ngs
Other
1 stars 3 forks source link

Upgrade to Ubuntu 16.04 and some updates #27

Closed biocyberman closed 7 years ago

biocyberman commented 7 years ago

I upgraded to Ubuntu 16.04 because Ubuntu 15.04 is not available for download anymore from the default Docker hub.

Some other updates are explained in the commit messages.

Docker build ran successfully when running the following command inside docker directory, even though I haven't check with GATK and Novoalign stuffs: tar -czh . | docker build --rm --build-arg VIRAL_NGS_VERSION=1.15.4 -

I think there is still room for improvement on the Dockerfile so that we can omit the --rm argument when building, thereby reduce build time. Currently the steps where docker download and install conda packages are the longest ones.

tomkinsc commented 7 years ago

Thanks for putting in the time to look at this. You mention "Ubuntu 15.04 is not available for download anymore from the default Docker hub." When was Ubuntu 15.04 removed from the default Docker Hub? We successfully built the Dockerfile with Ubuntu 15.04 two hours ago (viral-ngs tag 1.15.4).

That said, I would not be opposed to moving to an LTS base image like 16.04. I'm not sold on phusion/baseimage however. IMHO the viral-ngs image does not need the custom Phusion init system (we are process-focused, and are not forking background processes as say, an apache container would). Additionally, phusion seems slow to update their base image in response to security vulnerabilities (last push is 8 months ago for phusion/baseimage vs 3 days ago for library/ubuntu).

How specifically, does the viral-ngs image benefit from phusion/baseimage:0.9.19 over ubuntu:16.04?