Don't explicitly use PyEnsembl install

openvax / neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Apache License 2.0

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Closed iskandr closed 5 years ago

iskandr commented 5 years ago

Instead, run vaxrank with option --download-reference-genome-data, which will download/install Ensembl data required for annotating VCFs.

iskandr commented 5 years ago

Did we ever add this to the pipeline or does it still do a manual install of mouse & human references?

julia326 commented 5 years ago

Added this a while ago, closing out this issue