Using the container

This pages walks you though how to use the docker container and details some pre-configured settings.

Environment file

The docker container should run out of the box with the env/env.public environment file. However, you may want to use your own env file e.g., if you want to map data on your local machine to the container.

To do this, first make a copy of the env.public file and call it env. In the base directory run

cp env/env.public env/env

The env file is now your personal environment file and will be ignored by git. Make sure you change the PATH_TO_ENV to ../env/env so docker can find it. Then to run the docker container with your personal env file,

bash run.sh

Volumes

Volumes allow the docker container to see files (and live edits) on your local system.

By default the container has the ucsc_spectral_pipeline repository, where you launched the container from, mapped into /home/ucsc_spectral_pipeline/ in the container.

Also by default the container has the ucsc_spectral_pipeline/extra_files/disp.cl mapped to /etc/iraf/disp.cl in the container, and ucsc_spectral_pipeline/login.cl is mapped to /etc/iraf/login.cl in the container.

You might want to mount your own data volumes in the container. To do this set the DATA_VOLUME variable in your env file to the path on your local machine container the data. This data will then be available in the docker container at /home/data/.

Running the pipeline

To run a pipeline script run when in the container.

python3 ${PIPELINE}/<name_of_script>.py

Running pyraf

To run pyraf in the container,

pyraf

You should see the pyraf GUI. If you get an “cannot find X display error”, stop the container and run “xhost +localhost” on your machine.