This tutorial demonstrates how to containerize a simple pca plotting script using Docker.
- Docker
- Git
Clone the repository:
git clone https://github.com/LukeAndersonTrocme/pcb_docker.git
cd pcb_docker
Be sure to navigate to the root directory of the project where the Dockerfile is located. Then build the Docker image:
docker build -t pca_plotter .
This command tells Docker to build an image named pca_plotter based on the instructions in the Dockerfile located in the current directory (.).
Run the Docker container by mounting the data directory to the /data directory inside the container.
docker run --rm -v $(pwd)/data:/data pca_plotter
This command does the following:
docker run tells Docker to run a container.
--rm instructs Docker to remove the container once it stops running.
-v $(pwd)/data:/data mounts the data directory from your project to the /data directory in the container.
$(pwd) is replaced by your current directory path, making sure your pca.csv file is accessible to the script inside the container.
pca_plotter is the name of the Docker image to run.
This docker image took 6 minutes to build on my laptop:
luke$ docker build -t pca_plotter .
[+] Building 392.7s (10/10) FINISHED
=> [internal] load build definition from dockerfile 0.0s
=> => transferring dockerfile: 528B 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/library/r-base:latest 0.7s
=> CACHED [1/5] FROM docker.io/library/r-base:latest@sha256:89665d00ab6ec19ee1b6c64d94f8de1f376b0db04fb7f52c7757 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 1.46kB 0.0s
=> [2/5] RUN R -e "install.packages(c('ggplot2', 'cowplot'), dependencies=TRUE)" 391.4s
=> [3/5] COPY scripts/plot_pca.r /usr/local/bin/plot_pca.r 0.0s
=> [4/5] RUN chmod +x /usr/local/bin/plot_pca.r 0.1s
=> [5/5] WORKDIR /data 0.0s
=> exporting to image 0.5s
=> => exporting layers 0.5s
=> => writing image sha256:e360f59af47df43bf8983283f9a4c0fdfda38d457ebe875744617923dc601035 0.0s
=> => naming to docker.io/library/pca_plotter 0.0s
The data are downloaded from gnomad (Sample metadata TSV)
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