A collection of functions to execute NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers. To install it you can use use devtools:
install.packages("devtools")
library(devtools)
install_github("kendomaniac/docker4seq", ref="master")
##Requirements You need to have docker installed on your machine, for more info see this document: https://docs.docker.com/engine/installation/. docker4seq package is expected to run on 64 bits linux machine with at least 4 cores and 32 Gb RAM. A scratch folder should be present, e.g. /data/scratch and it should be writable from everybody:
chmod 777 /data/scratch
The functions in docker4seq package require that user is sudo or part of a docker group. See the following document for more info: https://docs.docker.com/engine/installation/linux/ubuntulinux/#/manage-docker-as-a-non-root-user
IMPORTANT The first time docker4seq is installed the downloadContainers needs to be executed to download to the local repository the containers that are needed for the use of docker4seq
More info on the functionalities of the package are available at: http://rpubs.com/rcaloger/280163
In case you wish to use MAC OS or windows you need to install https://www.docker.com/products/docker-toolbox and run within the Docker Quickstart Terminal.app