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>
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 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.
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
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.
> 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.
To run nose tests navigate into
` cd tests && nosetests -s `
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