Submitted originally by: katie.shakman
When setting up a new compute environment in Domino, the best practice in Domino is to use and build off of our Domino base images. More about our Domino base images here: https://docs.dominodatalab.com/en/4.1/reference/environments/Domino_4_standard_environments.html
However, sometimes you may want to experiment with a third-party Docker image in Domino. One way to do this is to look at what packages are installed, and add them to your favorite Domino compute environment. But sometimes you might want to try to just import and use it with minimal modification. Your results may vary depending on the specifics of what's in your Docker image, but these guidelines will help you to import your desired image with the fewest changes possible:
- Determine what operating system the image uses. Domino supports Ubuntu, CentOS, and RHEL images.
- Create a new compute environment and specify your 3rd-party Docker image using the Custom image option. Example shown below for the crisprlab/crisprdisco image:
Once you save, it will show up like this on the Environment Definition page:
- Set up the ubuntu user. Domino requires userid host machine has match userid docker image. By convention, most ubuntu hosts use username ubuntu. You can enforce this adding following top Dockerfile instructions when you build your image:
USER root # Create the Ubuntu user RUN \ groupadd -g 12574 ubuntu && \ useradd -u 12574 -g 12574 -m -N -s /bin/bash ubuntu
Screenshot showing where to add this on the compute environment page:
- Ensure that pip is installed in the environment. If needed, you can add the following to the Dockerfile instructions to install pip:
RUN apt-get update && apt-get install -y \ python-pip RUN pip install --upgrade pip
- [If you just want to run scripts/bash jobs non-interactively, you can skip this step. ] If interactive workspaces are desired, such as Jupyter, set them up as described here: https://docs.dominodatalab.com/en/latest/reference/environments/Adding_new_workspaces_with_pluggable_notebooks.html. If you encounter any issues with this step, particularly if you are using an image with an older version of Python (<Py 3.x), you may need to install additional dependencies and a Python 3.x version (this won't uninstall your 2.7 version, so you can still use that in a terminal from your interactive workspace). Try adding the snippet below to your Dockerfile instead of the snippet from the docs:
USER root RUN apt-get update -y #### Jupyter dependencies #### RUN apt-get install -y libzmq3-dev pandoc pandoc-citeproc libssl-dev libsqlite3-dev unzip && \ apt-get install zlib1g-dev && \ apt-get install python-setuptools -y && \ apt-get install python-tk -y #### Install python 3.x #### RUN cd /tmp && \ wget -q https://www.python.org/ftp/python/3.6.8/Python-3.6.8.tgz && \ tar -xzf Python-3.6.8.tgz && \ cd Python-3.6.8 && ./configure && make && make install && rm -rf /tmp/* #### Set python version #### RUN rm /usr/bin/python && \ ln -s /usr/local/bin/python3 /usr/bin/python RUN cd /tmp && curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py RUN rm -rf /opt/conda/bin/pip && \ ln -s /usr/bin/pip3 /opt/conda/bin/pip && \ pip install --upgrade pip #### Installing Notebooks,Workspaces,IDEs,etc #### # Clone in workspaces install scripts # Add workspace configuration files RUN \ cd /tmp && \ wget -q https://github.com/dominodatalab/workspace-configs/archive/2019q4-v1.zip && \ unzip 2019q4-v1.zip && \ cp -Rf workspace-configs-2019q4-v1/. /var/opt/workspaces && \ rm -rf /var/opt/workspaces/workspace-logos && rm -rf /tmp/workspace-configs-2019q4-v1 && \ ### Install Jupyter from workspaces chmod +x /var/opt/workspaces/jupyter/install && \ /var/opt/workspaces/jupyter/install && \ ### Clear apt list to save space rm -rf /var/lib/apt/lists/*
Then build and test your environment.
If you have trouble installing pip, and
lsb_release -ashows that you are using Ubuntu 20.04, then follow the instructions here: https://stackoverflow.com/questions/61981156/unable-to-locate-package-python-pip-ubuntu-20-04
Specifically, from user Expired Brain, try this:
Pip for Python 2 is not included in the Ubuntu 20.04 repositories.
You need to install pip for Python 2 using the get-pip.py script.
1. Start by enabling the universe repository:
2. Update the packages index and install Python 2:
3. Use curl to download the get-pip.py script:
4. Once the repository is enabled, run the script as sudo user with python2 to install pip :
Submitted by: katie.shakman
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