R2g Docker

Introduction

Reads to genes, or r2g, is a computationally lightweight and homology-based pipeline that allows rapid identification of genes or gene families from raw sequence databases in the absence of an assembly, by taking advantage of over 10,000 terabases of sequencing data for all kinds of species deposited in Sequence Read Archive hosted by National Center for Biotechnology Information, which can be effectively run on most common computers without high-end specs.

You can find source code of the r2g project here.

This docker integrates required third-party applications and the r2g itself, which is ready to go.

Running the images

Print detailed usages

docker run -it -v /dev/shm:/dev/shm -v /dir/to/your/folder:/workspace -u $UID yangwu91/r2g:latest --help

To avoid the applications crashing inside a docker container, the option -v /dev/shm:/dev/shm is recommended to be used, or tune the value --shm-size=8g in your specific cases.

In the command, the option -v /dir/to/your/folder:/workspace will mount your folder /dir/to/your/folder onto the Docker.

Debug mode

Enter an interactive shell to debug:

docker run -it yangwu91/r2g:latest debug

An example command

docker run -it -v /dev/shm:/dev/shm -v /dir/to/your/folder:/workspace yangwu91/r2g:latest -o OUTPUT -s SRXNNNNNN -q QUERY.fasta --cut 80,50 -p blastn

After that, you can find the results in the folder /dir/to/your/folder/OUTPUT/.