Setup

NOTE

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.

• Setup
• Requirements
  • Optional requirements
• Installation
• Running ELLA anno
• Annotate options

Requirements

• Docker (opens new window)
• make (apt install make, yum install make, apk add make, etc.)

Optional requirements

• Singularity (opens new window)
• Buildkit (opens new window)
• Supervisor (opens new window)

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 run
• 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)