Build docker image on Ubuntu to match VEP dockerfile

[EdGreen21]

Development Suggestion Base container on Ubuntu 16:04 instead of miniconda

Benefits 1 - The ENSEMBL VEP dockerfile link is based on Ubuntu16.04, allowing a multi-stage docker build to make a container that can process *.vcf files as well as later pVACtoolssteps.

2 - pvactools can be installed using pip; Ubuntu16.04 ships with Python 3.5, so potentially avoid need for need for conda environments.

3 - ability to combine with other Ubuntu based builds such as this one allowing full XRDP support, making the pvacviz GUI easily accessible. Alternative would be to alter the pvacviz code (as suggested in pvactools issue #257 here) to potentially host to access pvacvizbrowser using port forwarding.

Potential Costs If there are remaining conda dependencies in pvactools this would require the installation of miniconda in the docker file, following the guidelines in the miniconda dockerfile here but adding maintenance overhead

[susannasiebert]

conda is required in this image for IEDB since it runs on python2.7. A docker container for VEP with the plugins needed for pVACseq is available here: https://hub.docker.com/r/mgibio/vep/

[EdGreen21]

Thanks Susanna, that also had the

RUN wget https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/90/Downstream.pm

line that I was looking for