Corrections needed to rabix installation instructions

[maryawood]

I'm currently working on setting up CloudNeo for use with rabix, and I wanted to let you know that the installation instructions need updating.

For the netMHC and netMHCpan installations, the softwares should be downloaded to the main CloudNeo directory in order to use the recommended docker image build commands as specified in the wiki (which need a '-f' in front of the docker file paths, too).

This command within the Dockerfile for each of these tools was also giving me trouble:

RUN apt-get install -y python-biopython

but I was able to use

RUN wget https://bootstrap.pypa.io/get-pip.py

RUN python get-pip.py

RUN pip install biopython

instead, and it worked fine. Not sure if this is an issue on my end or a more general issue, though.

The polysolver build also requires a lot of files that aren't in the repository and must be tracked down (e.g. GATK v3.5 jar, mutect jar, etc.).

It's fairly doable to figure out these issues out on your own, but it would be good to have more accurate and thorough instructions in the wiki.

[maryawood]

Also the BWA indexes in the HLAminer data base are incompatible with the version of BWA installed by the BWA dockerfile, so the fastas in that database need to be reindexed with BWA v-0.7.13 prior to running the workflow