Fluidigm2PURC on Docker

We have made the Fluidigm2PURC pipeline available as a Docker image in the hopes that it will facilitate its use by providing all dependencies pre-installed. This also allows any researcher with the Docker software installed on their computer to use our pipeline (e.g., Fluidigm2PURC won’t work on Windows without using Docker). Details on Docker itself can be found on the main website: link.

To obtain the Fluidigm2PURC image, first download Docker for your computer (if you haven’t already done so). Then, launch a terminal window and use the following commands to get the software:

docker pull pblischak/fluidigm2purc

To run an analysis with Fluidigm2PURC, launch a Docker container that is running the Fluidigm2PURC image:

docker run -it pblischak/fluidigm2purc

The above line of code will get you running inside a Docker container with everything that you need to run Fluidigm2PURC. However, you will also need to link your local files to the container. This can be done using the -v option. To start, navigate to the folder with your paired-end reads (R1 and R2) that you want to analyze with Fluidigm2PURC. Then, use this command to link that folder to the Docker container running Fluidigm2PURC:

docker run -it -v $(pwd):/home pblischak/fluidigm2purc

If you type ls, you should see your files available for analyzing. All analyses that you run in the container will also write those files to the directory from which you launched the container. This way, everything that you do will automatically be available on your computer outside of Docker.