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IBM Functional Genomics Platform SDK to explore data.

Project description

https://travis.ibm.com/GrandChallenge-Almaden/omxware-pypi.svg?token=zra2vLszsZmyB2CQTsas&branch=master Latest Version

Web Services

https://ibm.biz/functional-genomics-api


SDK Documentation:

https://ibm.biz/functional-genomics-sdk-docs


Getting Started

https://ibm.github.io/omxware-pypi-docs/build/html/usage.html


Help / Forums

https://ibm.biz/functional-genomics-forum


Citation


Use with Docker

In an effort to make it easier for users and developers to get started with IBM Functional Genomics Platform (previously ‘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

docker run -it --rm --name omxware -v "$(pwd):/opt/my_work" c0mpiler/alpine-omxware-base:latest ash


2) JupyterLab: docker pull c0mpiler/jupyter:latest

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

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