DiscoveryDocker

This version is not longer updated here, for an updated version of the pipeline visit FHI's github

Description

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Installation

git clone https://github.com/garcia-nacho/DiscoveryDocker
cd DiscoveryDocker
docker build -t garcianacho/discoveryfhi .

Alternativetly, it is posible to pull updated builds from Dockerhub:

docker pull garcianacho/discoveryfhi

Running the pipeline

Navigate to the folder where the fastq files are located and run the following command

docker run -it --rm -v $(pwd):/home/docker/Discovery/Fastq garcianacho/discoveryfhi

Older versions of docker might require the flag --privileged to run.
Multiuser systems might require the flag -u 1000 (or other uid) to run.

Note that the current version supports only illumina sequences.