brainy-mind 0.2.1

brainy is a nimble workflow managing tool which is a part of iBRAIN framework for scientific computation primarily applied for BigData analysis in context of HPC and HTS

<p align=”center”><img src=”https://github.com/pelkmanslab/brainy/raw/master/ui/web/assets/images/brainy_logo.png” alt=”logo” height=”121” width=”121”></p>

##About brainy

brainy is a nimble workflow managing tool, at the core of [iBRAIN](https://github.com/pelkmanslab/iBRAIN/) functionality. It allows creation of projects according to the expected framework layout. It also oversees the execution of the projects and provides monitoring of any relevant progress of the conducted computation.

##iBRAIN

iBRAIN is a software framework for scientific computation primarily applied for BigData extraction and analysis in context of HPC and HTS as well as large bioinformatical analysis.

##Documentation

A really good place to understand what is brainy is to read the user manual:

• [User manual](https://github.com/pelkmanslab/brainy/wiki/User-Manual)

• [Developer Documentation](https://github.com/pelkmanslab/brainy/wiki/Developer-Documentation)

> Tip: get help about the commands you need by saying brainy help or brainy help project

##Getting started

Create you first project

` brainy create project PureAwesomeness --from demo `

Go inside the project folder and adjust settings in your pipelines. Afterwards run the project.

` cd PureAwesomeness # Adjust settings in .brainy <project settings> and hello.br <pipe description> YAML files brainy run project `

To see the report in your local web browser, do ` brainy ui serve `

If things are looking good, continue by submitting your project into the cloud. Find out how to do this in the [Cloud](https://github.com/pelkmanslab/brainy/wiki/User-Manual#Cloud) section of the brainy’s User Manual.

##Installation

> On Ubuntu (debian): sudo apt-get install python-setuptools git && sudo easy_install pip

> On Mac: brew install libyaml

>It is strongly recommended to use [conda](http://conda.pydata.org/docs/) as python 2.7+ environment.

The package is available on [PyPI](https://pypi.python.org/pypi/brainy-mind/).

` pip install brainy-mind `

To get the bleedding edge version you have to clone the repository and install brainy in developer mode from local folder:

` cd && git clone https://github.com/pelkmanslab/brainy cd brainy && pip install -e . `

Once installed, inspect the state of configuration in ~/.brainy/ folder.

Remember that you can generate ~/.brainy/config from the template again by

` brainy init config `

You will have to edit the template that has been copied according to your cluster scheduler settings and so on.

> Supported OS/platforms are Linux and Mac OSX.

##Tests

To run nose tests navigate into

` cd tests && nosetests -s `