fastqc-docker

Build a Container for bioconda fastqc

Steps to build this docker container.

1. Look up on anaconda the tool you wish to install
2. create an environment.yml file either manually or automatically
3. Use the template Dockerfile modifying if necessary (in our case we have no custom files for the src directory so we do not use that)
4. Build the Docker Image
5. Set up GitHub Actions

To edit the files:

1. Use a simple editor (Text Edit on Mac is fine) - we want to be cautious about unseen characters
2. Use emacs (can be installed with conda)

conda install -c conda forge emacs

To build your image from the command line:

• Can do this on Google shell - docker is installed and available

docker build -t fastqc .

To test this tool from the command line

Set up an environment variable capturing your current command line:

PWD=$(pwd)

Then mount and use your current directory and call the tool now encapsulated within the environment.

docker run -it -v $PWD:$PWD -w $PWD fastqc fastqc -h