The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.
This Docker image contains tools needed to run MMTF (Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.)
Part of the 2018 UCSD Structural Bioinformatics Hackathon - https://github.com/sbl-sdsc/mmtf-workshop-2018
From the host, connect to an AWS instance
### Replace [email protected] with your AWS Public DNS
ssh -i "/path/to/sshkey.pem" -L 8888:0.0.0.0:8888 [email protected]
From AWS (ubuntu) instance, install docker and run
### install Docker if needed
sudo apt-get update
sudo apt-get install -y docker.io
### run Docker image from a directory containing your Jupyter Notebook or clone it
git clone https://github.com/sbl-sdsc/mmtf-workshop-2018.git
docker run -it --rm -v `pwd`:`pwd` -w `pwd` -p 8888:8888 stevetsa/mmtf-docker
## Open a read-only Jupyter notebook stored in the container
## docker run -it --rm -w /home/jovyan/work -p 8888:8888 stevetsa/mmtf-docker
Point browser to http://localhost:8888/?token=abc........ (Last line of output from the previous command)
Small base image for defining your own stack
- Minimally-functional Jupyter Notebook 5.2.x (e.g., no pandoc for document conversion)
- Miniconda Python 3.x
- No preinstalled scientific computing packages
- Unprivileged user
jovyan(uid=1000, configurable, see options) in groupusers(gid=100) with ownership over/home/jovyanand/opt/conda - tini as the container entrypoint and start-notebook.sh as the default command
- A start-singleuser.sh script useful for running a single-user instance of the Notebook server, as required by JupyterHub
- A start.sh script useful for running alternative commands in the container (e.g.
ipython,jupyter kernelgateway,jupyter lab) - Options for a self-signed HTTPS certificate and passwordless
sudo
The following command starts a container with the Notebook server listening for HTTP connections on port 8888 with a randomly generated authentication token configured.
docker run -it --rm -p 8888:8888 jupyter/base-notebook
Take note of the authentication token included in the notebook startup log messages. Include it in the URL you visit to access the Notebook server or enter it in the Notebook login form.
The Docker container executes a start-notebook.sh script script by default. The start-notebook.sh script handles the NB_UID, NB_GID and GRANT_SUDO features documented in the next section, and then executes the jupyter notebook.
You can launch JupyterLab by setting JUPYTER_ENABLE_LAB:
docker run -it --rm -e JUPYTER_ENABLE_LAB=1 --rm -p 8888:8888 jupyter/base-notebook
You can pass Jupyter command line options through the start-notebook.sh script when launching the container. For example, to secure the Notebook server with a custom password hashed using IPython.lib.passwd() instead of the default token, run the following:
docker run -d -p 8888:8888 jupyter/base-notebook start-notebook.sh --NotebookApp.password='sha1:74ba40f8a388:c913541b7ee99d15d5ed31d4226bf7838f83a50e'
For example, to set the base URL of the notebook server, run the following:
docker run -d -p 8888:8888 jupyter/base-notebook start-notebook.sh --NotebookApp.base_url=/some/path
For example, to disable all authentication mechanisms (not a recommended practice):
docker run -d -p 8888:8888 jupyter/base-notebook start-notebook.sh --NotebookApp.token=''
You can sidestep the start-notebook.sh script and run your own commands in the container. See the Alternative Commands section later in this document for more information.
You may customize the execution of the Docker container and the command it is running with the following optional arguments.
-e GEN_CERT=yes- Generates a self-signed SSL certificate and configures Jupyter Notebook to use it to accept encrypted HTTPS connections.-e NB_UID=1000- Specify the uid of thejovyanuser. Useful to mount host volumes with specific file ownership. For this option to take effect, you must run the container with--user root. (Thestart-notebook.shscript willsu jovyanafter adjusting the user id.)-e NB_GID=100- Specify the gid of thejovyanuser. Useful to mount host volumes with specific file ownership. For this option to take effect, you must run the container with--user root. (Thestart-notebook.shscript willsu jovyanafter adjusting the group id.)-e GRANT_SUDO=yes- Gives thejovyanuser passwordlesssudocapability. Useful for installing OS packages. For this option to take effect, you must run the container with--user root. (Thestart-notebook.shscript willsu jovyanafter addingjovyanto sudoers.) You should only enablesudoif you trust the user or if the container is running on an isolated host.-v /some/host/folder/for/work:/home/jovyan/work- Mounts a host machine directory as folder in the container. Useful when you want to preserve notebooks and other work even after the container is destroyed. You must grant the within-container notebook user or group (NB_UIDorNB_GID) write access to the host directory (e.g.,sudo chown 1000 /some/host/folder/for/work).--group-add users- use this argument if you are also specifying a specific user id to launch the container (-u 5000), rather than launching the container as root and relying on NB_UID and NB_GID to set the user and group.
You may mount SSL key and certificate files into a container and configure Jupyter Notebook to use them to accept HTTPS connections. For example, to mount a host folder containing a notebook.key and notebook.crt:
docker run -d -p 8888:8888 \
-v /some/host/folder:/etc/ssl/notebook \
jupyter/base-notebook start-notebook.sh \
--NotebookApp.keyfile=/etc/ssl/notebook/notebook.key
--NotebookApp.certfile=/etc/ssl/notebook/notebook.crt
Alternatively, you may mount a single PEM file containing both the key and certificate. For example:
docker run -d -p 8888:8888 \
-v /some/host/folder/notebook.pem:/etc/ssl/notebook.pem \
jupyter/base-notebook start-notebook.sh \
--NotebookApp.certfile=/etc/ssl/notebook.pem
In either case, Jupyter Notebook expects the key and certificate to be a base64 encoded text file. The certificate file or PEM may contain one or more certificates (e.g., server, intermediate, and root).
For additional information about using SSL, see the following:
- The docker-stacks/examples for information about how to use Let's Encrypt certificates when you run these stacks on a publicly visible domain.
- The jupyter_notebook_config.py file for how this Docker image generates a self-signed certificate.
- The Jupyter Notebook documentation for best practices about running a public notebook server in general, most of which are encoded in this image.
The default Python 3.x Conda environment resides in /opt/conda.
The commands jupyter, ipython, python, pip, and conda (among others) are available in both environments. For convenience, you can install packages into either environment regardless of what environment is currently active using commands like the following:
# install a package into the default (python 3.x) environment
pip install some-package
conda install some-package
The start.sh script supports the same features as the default start-notebook.sh script (e.g., GRANT_SUDO), but allows you to specify an arbitrary command to execute. For example, to run the text-based ipython console in a container, do the following:
docker run -it --rm jupyter/base-notebook start.sh ipython
Or, to run JupyterLab instead of the classic notebook, run the following:
docker run -it --rm -p 8888:8888 jupyter/base-notebook start.sh jupyter lab
This script is particularly useful when you derive a new Dockerfile from this image and install additional Jupyter applications with subcommands like jupyter console, jupyter kernelgateway, etc.
You can bypass the provided scripts and specify your an arbitrary start command. If you do, keep in mind that certain features documented above will not function (e.g., GRANT_SUDO).