<commit_before>![Build Status](https://travis-ci.org/rabix/rabix.svg?branch=devel)

## Reproducible Analyses for Bioinformatics 

Rabix is an open source implementation of the specification being developed on the
 [Common Workflow Language mailing list](https://groups.google.com/forum/#!forum/common-workflow-language).

CWL is an informal task force consisting of people from various organizations that have an interest in portability
 of bioinformatics workflows.
The goal is to specify a way to describe bioinformatics tools and workflows that is powerful,
 easy to use and allows for portability of tools/workflows and reproducibility of runs.

To play with describing tools and making workflows visit [rabix.org](http://rabix.org).

This repo includes a local python executor and some utilities for building docker images.


### Install

Rabix requires Python 2.7 or 3.x to run.

There are several external dependencies for Rabix.
The first one is [Docker](https://docs.docker.com/installation/#installation)
for running command line bioinformatics tools.
Second one is a JavaScript interpreter: 
you can look for available options on
[PyExecJS](https://github.com/doloopwhile/PyExecJS),
but probably the easiest  way is to install something like PhantomJS or NodeJS
from your distro's repo.
Finally you should install `libyaml` development package.

If you are on Debian-based ditro, the following should work:

```
$ sudo apt-get install phantomjs libyaml-dev
```
 
Second, install rabix via `pip`:

```<commit_msg>README improvements.<commit_after>![Build Status](https://travis-ci.org/rabix/rabix.svg?branch=devel)

## Reproducible Analyses for Bioinformatics 

Rabix is an open source implementation of the specification being developed on the
 [Common Workflow Language mailing list](https://groups.google.com/forum/#!forum/common-workflow-language).

CWL is an informal task force consisting of people from various organizations that have an interest in portability
 of bioinformatics workflows.
The goal is to specify a way to describe bioinformatics tools and workflows that is powerful,
 easy to use and allows for portability of tools/workflows and reproducibility of runs.

To play with describing tools and making workflows visit [rabix.org](http://rabix.org).

This repo includes a local python executor and some utilities for building docker images.


### Install

Rabix requires Python 2.7 or 3.x to run.

There are several external dependencies for rabix.
The first one is [Docker](https://docs.docker.com/installation/#installation)
for running command line bioinformatics tools.
Second one is a JavaScript interpreter: 
you can look for available options on
[PyExecJS](https://github.com/doloopwhile/PyExecJS),
but probably the easiest  way is to install something like PhantomJS or NodeJS
from your distro's repo.
Finally you should install `libyaml` development package.

If you are running Ubuntu, the following should setup your system:

```
$ sudo apt-get install python-dev python-pip docker.io phantomjs libyaml-dev
```

although you'll probably want to install newer version of Docker from the above link.
 
Now we can install rabix via `pip`:

```
{'fraction_non_alphanumeric': 0.06916064130776485, 'fraction_numerical': 0.001886199308393587, 'mean_word_length': 4.925512104283054, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 8, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6755261', 'n_tokens_mistral': 903, 'n_tokens_neox': 810, 'n_words': 387}