# Setup


This documentation is a work in progress and is incomplete.

Please contact developers for more details.

This page describes the setup process of ELLA anno.

# Requirements

# Optional requirements

# Installation

ELLA anno is available in both Docker and Singularity containers. It can also be set up to be used locally, but a container is recommended. We also recommend using buildkit (opens new window) for faster docker builds. You may see a warning about unconsumed arguments if you build the docker images without buildkit installed/enabled, but it doesn't negatively impact the images in any way.

Installation process:

  1. Clone the repo
    • git clone git@gitlab.com:alleles/ella-anno
  2. Check out the desired release
    • git checkout v2.0.0
  3. Build the docker images
    • make build
    • make build-annobuilder
  4. Download the annotation datasets
    • make download-data
  5. Generate singularity images (if desired)
    • make singularity-build

# Running ELLA anno

Start the container:

  • Docker: make anno
  • Singularity: make singularity-start

# Annotate options

Options in /src/annotation/annotate.sh

Option Explanation
--vcf [vcf] Input VCF
--hgvsc [hgvsc] Input HGVSC
--regions [regions] Regions to slice input on
--convert Flag to run conversion only, not annotation
-o/--outfolder [outfolder] Output folder (default: working directory)
-p/--processes Number of cores to use for time-consuming annotation steps (default number of cores available)
Last Updated: 3/27/2020, 11:24:52 AM