Docker Installation
ClusterScan can be also ran through the docker engine. Docker is an open source project intended to provide tools to performs operating-system-level virtualization also known as containerization. More information can be found here. In order to use ClusterScan in a docker container, you must install the docker engine and the docker ClusterScan image. You can find a complete Linux installation guide of the docker engine following this link.
If you already have the docker engine installed on your machine, you can skip this step. To install the docker engine you simply have to type:
curl -fsSL https://get.docker.com/ | sh
If you haven't curl installed, you can obtain it by typing:
sudo apt update
sudo apt install curl
Once you have the docker engine installed, you may want guarantee administrator permissions to your user:
sudo usermod -aG docker <your-user>
After this step you must exit and open a new terminal. You can test your docker engine installation with the command:
docker run hello-world
To obtain the latest ClusterScan docker image type:
docker pull sangeslab/clusterscan:latest
You can test your docker ClusterScan installation by typing:
docker images
obtaining something like that:
| REPOSITORY | TAG | IMAGE ID | CREATED | SIZE |
|---|---|---|---|---|
| sangeslab/clusterscan | latest | 1bc62465dc7c | 3 days ago | 1.44GB |
| hello-world | latest | f2a91732366c | 4 months ago | 1.85kB |
To get rid of the ClusterScan image:
docker rmi -f sangeslab/clusterscan
you can also remove the created containers by tracking their IDs:
docker ps -a
docker rm <your container ID>
To run ClusterScan type:
docker run --user $(id -u) -it -v /full/path/to/data/folder:/data sangeslab/clusterscan bash
and substitute /full/path/to/data/folder with the complete path to the directory containing your input data.
You can test whether CLusterScan is ready with:
clusterscan.py -h