redsnic/wgalp repository overview

⁠WGA-LP

A pipeline for bacterial whole genome assembly

This pipeline is linked to the following gitHub repositoy: WGA-LP⁠

⁠Recommended usage

This package is meant to create an Ubuntu environment with all the dependencies to run the pipeline. Because of this, the functionalities of the pipeline are offered from a shell accessible through docker exec. It is also expected that the user shares a folder with the Container to exchange input and output files.

# pull image
docker pull redsnic/wgalp
# run image: replace <HOST_SHARED_FOLDER> with a directory on your file system
docker run -itd -v <HOST_SHARED_FOLDER>:/root/shared --name wgalp redsnic/wgalp
# access shell
docker exec -it wgalp /bin/bash

Optional: To be able to create RAMdisks for the kraken2 database, a privileged container is needed. Replace the previous docker run command with the following:

docker run -itd -v <HOST_SHARED_FOLDER>:/root/shared --privileged --name wgalp redsnic/wgalp

as usual, use exit to quit the shell. Changes done inside the container are persistent.