OMXware - Base docker image to get started
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IBM Functional Genomics Platform (formerly 'OMXWare')
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In an effort to make it easier for users and developers to get started with OMXWare, We have a 2 base docker images with python and OMXWare pre-installed. It also comes with a bunch of python libs like matplotlib, numpy along with some others.
1) Minimal: docker pull c0mpiler/alpine-omxware-base:latest
.. code-block:: bash
docker run -it --rm --name omxware -v "$(pwd):/opt/my_work" c0mpiler/alpine-omxware-base:latest ash
* This is a relatively small docker image with just the required packages / libraries installed and setup.
* Change the mount point to whatever you want on you host machine.
* You may use this image as a base to build other docker containers / applications. Refer to: https://github.com/c0mpiler/alpine-omxware-base/blob/master/Dockerfile for specifics.
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2) JupyterLab: docker pull c0mpiler/jupyter:latest
.. code-block:: bash
docker run -d --name jupyter --restart always -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes \
-v /mnt/storage/jupyter:/home/jovyan/work c0mpiler/jupyter start.sh jupyter lab --LabApp.token=‘omxware’
* This image has JupyterLab pre-installed and setup with some example OMXWare Jupyter notebooks.
* Change the mount point ``/mnt/storage/jupyter`` to whatever you want on you host machine – so you can share files from your host with this docker image.
* This image also has some example Jupyter notebooks for you to look at and get started.
* Once you run the docker image – you can open up ``http://<host-name>:8888/lab?`` in your browser and the pwd is ``omxware``.
* The host-name is that of your host machine you run this docker image on. If you are running it on your laptop, the host-name is either ``localhost`` or ``0.0.0.0``
Web Services
http://ibm.biz/omxware-api <https://api.s2s-omxware.us-south.containers.appdomain.cloud/>_
SDK Documentation:
http://ibm.biz/omxware-sdk-docs <https://ibm.github.io/omxware-pypi-docs/>_
Getting Started
https://ibm.github.io/omxware-pypi-docs/build/html/usage.html <https://ibm.github.io/omxware-pypi-docs/build/html/usage.html>_
Help / Forums
http://ibm.biz/omxware-forum <https://forum.s2s-omxware.us-south.containers.appdomain.cloud>_
Citation
OMXWare Team via the Forums <http://ibm.biz/omxware-citation>_ for updated citation information prior to publishing or presenting OMXWare content.e.g: "OMXWare: Microbial Life at Scale" IBM Research, manuscript in preparation
Content type
Image
Digest
Size
348.9 MB
Last updated
over 6 years ago
docker pull c0mpiler/alpine-omxware-base