AnnotSV Container Images

Docker and Singularity container definitions for AnnotSV v3.5.5.

Included in the images:

• AnnotSV v3.5.5
• Exomiser REST prioritiser JAR (v14.1.0)
• Poetry (Python dependency manager)
• bedtools, bcftools, Java, Python 3

Not included — mount at runtime (~3.5GB total):

• Human/mouse annotation files
• Exomiser phenotype data (2406_phenotype.zip)

Downloading Annotations

Annotations (including Exomiser phenotype data) must be downloaded once on the host:

git clone --depth 1 --branch v3.5.5 https://github.com/lgmgeo/AnnotSV.git /tmp/AnnotSV
cd /tmp/AnnotSV && make PREFIX=. install && make PREFIX=. install-human-annotation
# For mouse: make PREFIX=. install-mouse-annotation

This creates the annotation directory at /tmp/AnnotSV/share/AnnotSV/ (~3.5GB). Use this path (or move it wherever you like) as the mount source below.

Docker

Pull from GitHub Container Registry

docker pull ghcr.io/kchennen/annotsv:3.5.5
# or latest
docker pull ghcr.io/kchennen/annotsv:latest

Build locally

docker build -t annotsv:3.5.5 .

Run

# Show help
docker run --rm ghcr.io/kchennen/annotsv:3.5.5

# Annotate a VCF (mount annotations + data)
docker run --rm \
  -v /path/to/annotations:/opt/AnnotSV/share/AnnotSV \
  -v /path/to/data:/data \
  ghcr.io/kchennen/annotsv:3.5.5 \
  -SVinputFile /data/input.vcf \
  -outputDir /data/output

Singularity

Pull SIF from GitHub Release (recommended)

Pre-built SIF files are attached to each GitHub Release.

# Download directly from the release
wget https://github.com/kchennen/AnnotSV/releases/download/v3.5.5/annotsv_3.5.5.sif

# Or convert from the GHCR Docker image
singularity pull annotsv_3.5.5.sif docker://ghcr.io/kchennen/annotsv:3.5.5

Build locally from Docker image

docker build -t annotsv:3.5.5 .
singularity build annotsv_3.5.5.sif docker-daemon://annotsv:3.5.5

Build from definition file

sudo singularity build annotsv_3.5.5.sif AnnotSV.def

Run

# Show help
singularity run annotsv_3.5.5.sif -help

# Annotate a VCF (bind-mount annotations + data)
singularity run \
  -B /path/to/annotations:/opt/AnnotSV/share/AnnotSV \
  -B /path/to/data:/data \
  annotsv_3.5.5.sif \
  -SVinputFile /data/input.vcf \
  -outputDir /data/output

Alternatively, use the -annotationsDir flag instead of mounting to the default path:

singularity run \
  -B /path/to/annotations:/annotations \
  -B /path/to/data:/data \
  annotsv_3.5.5.sif \
  -annotationsDir /annotations \
  -SVinputFile /data/input.vcf \
  -outputDir /data/output