https://github.com/darribas/nih_box

Vagrant config for NIH project
https://github.com/darribas/nih_box

Last synced: 4 days ago
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Vagrant config for NIH project

• Host: GitHub
• URL: https://github.com/darribas/nih_box
• Owner: darribas
• License: other
• Created: 2015-01-25T00:54:50.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2015-01-25T12:39:20.000Z (about 10 years ago)
• Last Synced: 2025-01-19T03:42:13.920Z (7 days ago)
• Language: Shell
• Size: 133 KB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# NIH box

Vagrant setup to build a linux box loaded with required packages for NIH

project. This includes the following stacks:

* SciPy stack (`IPython` notebook, `matplotlib`, `pandas`, `scipy`...)

* Spatial regression in Python (`PySAL`)

* PyMC-3

* rmagic for the IPython notebook to interact with R

* R stack for multilevel and bayesian regression analysis (`lme4`,

  `MCMCpack`...)

## Usage

* Make sure you have installed a recent version of

  [`VirtualBox`](https://www.virtualbox.org/) and

  [`Vagrant`](https://www.vagrantup.com/).

* Clone this repository and navigate into the folder.

* Run `vagrant up`. The first time, this will build the box (so it might take

  a while, depending on connection and power of your machine). Once built, it

  will only take a few seconds to make it boot up.

* At this point, the virtual machine (VM) is running and an IPython notebook server

  is running. You can access it on the host by pointing your browser to

  [http://localhost:8888](http://localhost:8888)

* When you run `vagrant up`, it will also check if your folder has a subfolder

  called `notebooks` and, if not, it will create it. That is where the

  IPython notebook server will start running.

* When you are done with your analysis, `Ctr+C` twice will stop the notebook

  server. Then run `vagrant halt` to stop the VM.

* If you want to get rid of the VM, run `vagrant destroy` and things will

  dissapear as if they'd never happened. That easy.

## License and creadits

This is released under a BSD-type open-source license. 

This project was influenced and inspired by the

[`pysalREST`](https://github.com/pysal/pysalREST/tree/master/Vagrant) Vagrant

setup and by Lincoln Mullen's

[`vagrant-r-dev`](https://github.com/lmullen/vagrant-r-dev).