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extends mini-readme
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MattWellie committed Sep 26, 2023
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11 changes: 9 additions & 2 deletions images/ensembl-vep/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,22 @@ FROM ensemblorg/ensembl-vep:${VERSION}

USER root

# This Dockerfile is a departure from the style used in images/vep
# This Dockerfile is a departure from the style used in `images/vep`
# Instead of building up a fresh VEP install using Miniconda, we are
# using the official VEP image and adding plugins and data files to it.
# This is being built in parallel to the existing `vep` image so that we
# can maintain the existing image for backwards compatibility, and only
# switch once the newer VEP version has been evaluated.

# The AlphaMissense plugin at time of writing (26.09.2023) is available
# in the vep-plugin repository, but not installed within the latest image
# the PLI, LoF, & UTR annotator data files are not available by default,

# The PLI, LoF, & UTR annotator data files are not available by default,
# but only add minimally to the image size.

# LOFTEE is installed by default, but the standard version doesn't work
# for GRCh38, so we overwrite the standard files

# GCSfuse and the Google Cloud SDK are not installed, as the workflow
# using this image is intended to mount data files from GCS using Hail
# Batch, so that functionality is not required inside the image.
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