irfpy.aspera stable version on Docker

The stable version of the Dockerfile is at https://irfpy.irf.se/projects/aspera/Dockerfile

Create an image

To create an image, you can use the command

docker build -t irfpy/aspera https://irfpy.irf.se/projects/aspera/Dockerfile

Running ipython

To run the container, you may need to optimize some parameters.

• data_location: The location where irfpy dataset is stored.

• local_work_directory: The local working directory.

docker run -it \
        -v <data_location>:/Volumes/scidata/data \
        -v <local_work_directory>:/notebooks irfpy/aspera \
        ipython

For example, you may use

docker run -it --rm \
        -v /Volumes/scidata256/data:/Volumes/scidata/data \
        -v $(pwd):/notebooks irfpy/aspera \
        ipython

Then ipython is launched.

In [1]: import irfpy.aspera
In [2]: print(irfpy.aspera.__version__)
4.3.14

Running Jupyter Notebook

To run the Jupyter notebook, one should also specify the local port to be opened.

• local_port: The listening port for Jupyter.

docker run --rm -it \
        -p <local_port>:8888 \
        -v <data_location>:/Volumes/scidata/data \
        -v <local_work_directory>:/notebooks irfpy/aspera \
        bash -c "/opt/conda/bin/jupyter notebook --notebook-dir=/notebooks --ip=0.0.0.0 --port=8888 --no-browser --allow-root"

For example,

docker run --rm -it \
        -p 8888:8888 \
        -v /Volumes/scidata256/data:/Volumes/scidata/data \
        -v $(pwd):/notebooks irfpy/aspera \
        bash -c "/opt/conda/bin/jupyter notebook --notebook-dir=/notebooks --ip=0.0.0.0 --port=8888 --no-browser --allow-root"

Then, you can connect to the localhost with the specified local port: http://127.0.0.1:8888/?token=6a39e5adb9c49093cf589015af14a36e102ad81cf62f98ad Note that the token changes every time.