Installation

Quick start with Docker

The easiest way to run arcade is via Docker:

# Pull the image
docker pull fhlassen/arcade:latest

# Run a tool (mount current directory to /data)
docker run -v $PWD:/data fhlassen/arcade interpret_phase --help

All tools are available in the Docker image. To run commands on local files, mount the relevant directory:

docker run -v $PWD:/data fhlassen/arcade \
    interpret_phase \
        --geno /data/genotypes.txt.gz \
        --gene-map /data/gene_map.txt \
        > results.txt

Building from source

Pre-requisites

• g++ with C++11 support
• htslib (>= 1.19 recommended)
• zlib
• make

On macOS (Homebrew):

brew install htslib

On Ubuntu/Debian:

sudo apt-get install libhts-dev zlib1g-dev

Compile and install

git clone https://github.com/frhl/call_chets.git
cd call_chets
make
sudo make install

This installs the following executables to /usr/local/bin:

Executable	Description
interpret_phase	Compound heterozygote caller
make_pseudo_vcf	Pseudo-variant VCF generator
recode	Genotype recoder/orthogonalizer

To install to a custom location:

make install PREFIX=/path/to/install

Verify installation

interpret_phase --help
recode --help

External dependencies

arcade requires bcftools for the genotype extraction step of the gene-level pipeline. bcftools is not bundled with arcade but is available via most package managers:

# macOS
brew install bcftools

# Ubuntu/Debian
sudo apt-get install bcftools