biokepi pVAC-Seq

I want to compare the output of vaxrank and pVAC-Seq, would it be possible to get it into Biokepi?

Sep 26 '16 14:09 iskandr

Running seems easy, http://pvac-seq.readthedocs.io/en/latest/run.html

Installation we've seen similar before: http://pvac-seq.readthedocs.io/en/latest/install.html

@armish : is the .5 in python 3.5 important? what do we have by default when we get ``Python3`? https://github.com/hammerlab/biokepi/blob/master/src/environment_setup/conda.mli#L26

Sep 26 '16 15:09 smondet

sorry @smondet — completely missed this conversation. We do get 3.5 from a ``Python3 environment. We currently delegate that decision about which specific Python version to install to conda and only specify the major release number (2or3`).

Oct 04 '16 03:10 armish

BTW: just looking at their documentation, looks they expect a VEP-annotated single-sample VCF containing transcript, Wildtype protein sequence, and Downstream protein sequence information as an input to their pipeline. This means we have to install the lovely Perl script VEP as a pre-requisite to this.

Oct 05 '16 20:10 armish