robsyme/cegma-docker repository overview

⁠CEGMA in a Docker Container

Setting up a CEGMA installation can sometimes be a pain. This Dockerfile will build a container for CEGMA and all of its dependencies.

Let's say I have some data at /path/to/data/scaffolds.fasta. If you have docker, it's as easy as:

cd /path/to/data
docker run -v `pwd`:/data -w /data robsyme/cegma-docker:latest cegma -g scaffolds.fasta

This will download the latest cegma-docker image⁠ from index.docker.io, make a new container, mount the host directory inside the container and run cegma on the file 'scaffolds.fasta', just as if you'd installed cegma and all it's dependencies yourself on the host. When cegma is finished, docker closes the container. If you want docker to delete the container when cegma is done, just add '--rm=true'. Note that this won't delete your cegma results, just the container.

If you're on ubuntu 14.04 and don't have docker, you can install it with the incantation

sudo apt-get install docker.io
sudo ln -sf /usr/bin/docker.io /usr/local/bin/docker

If you're not on Ubuntu 14.04, the Docker people have you covered⁠.

Maybe you don't like the way I've set up the container (no worries, I understand). If so, you can simply take the Dockerfile from this repo, make changes and build it yourself

git clone https://github.com/robsyme/cegma-docker.git
cd cegma-docker
env editor Dockerfile # Make changes to your heart's content
docker build -t cegma:v2.5 .
docker run -it cegma:v2.5 bash