Metadata-Version: 1.1
Name: BanzaiDB
Version: 0.1.2
Summary: Database for Banzai NGS pipeline tool
Home-page: http://github.com/mscook/BanzaiDB
Author: Mitchell Stanton-Cook
Author-email: m.stantoncook@gmail.com
License: ECL 2.0
Description: .. image:: https://raw.github.com/mscook/BanzaiDB/master/misc/BanzaiDB.png
            :alt: BanzaiDB logo
        
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        .. image:: http://gitshields.com/v2/drone/github.com/mscook/BanzaiDB/brightgreen-red.png
           :target: https://drone.io/github.com/mscook/BanzaiDB
           :alt: Build status (Drone.io)
        
        (Using landscape.io and drone.io)
        
        
        What is BanzaiDB?
        -----------------
        
        **Please use the releases (https://github.com/mscook/BanzaiDB/releases). All 
        versions including most recent made some significant assumptions that are 
        currently being improved.**
        
        BanzaiDB is a tool for pairing Microbial Genomics Next Generation Sequencing 
        (NGS) analysis with a NoSQL_ database. We use the RethinkDB_ NoSQL database.
        
        BanzaiDB:
            * initialises the NoSQL database and associated tables,
            * populates the database with results of NGS experiments/analysis and,
            * provides a set of query functions to wrangle with the data stored within 
              the database.
        
        
        Why BanzaiDB?
        -------------
        
        The analysis (primary/secondary/tertiary) of large collections of draft 
        microbial genomes from NGS typically generates many separate flat files. 
        
        The bioinformatician will:
            * write scripts to parse and extract the important information from 
              the results files (often trying to standardise the output from 
              similar programs),
            * store these results in further flat files,
            * write scripts to link the results of one analysis step to another,
            * store these results in further flat files,
            * modify scripts as hypothesis is improved as a direct consequence of
              incorporating the knowledge from the previous steps,
            * ...
            * ...
            * ...
            * end up with thousands of flat files, many scripts and generally get 
              confused as to how and where everything came from.
        
        **The idea around BanzaiDB is to run once, store once analyse many times.**
        
        
        About BanzaiDB
        --------------
        
        BanzaiDB is geared towards outputs of Bioinformatics software employed by 
        the `Banzai NGS pipeline`_. 
        
        BanzaiDB is thus geared towards handling data generated from:
            * Velvet and SPAdes (assembly), 
            * BWA and Nesoni (mapping/variant calling),
            * Mugsy (whole genome alignment), 
            * BRATTNextGen (recombination detection) and,
            * Prokka (annotation).
        
        *The present focus is on storing and manipulating the results of SNP and 
        recombination analysis.*
        
        **Banzai is not a stable API.** 
        
        See the ReadTheDocs site for `BanzaiDB documentation`_ (User & API).
        
        
        About RethinkDB
        ---------------
        
        We choose RethinkDB_ as our underlying database for a few reasons:
            * RethinkDB is both developer and operations friendly. This sits well with 
              the typical bioinformatician,
            * NoSQL databases allow for a flexible schema. We can store/collect now, 
              think later. This is much like how science is performed.
            * Not every bioinformatician or lab has a system administrator. RethinkDB 
              is easy to setup and administer
            * We don't know how big our complex our datasets could get in the future. 
              It is easy to scale RethinkDB into a cluster.
            * ReQL the underlying query language is nice and simple to
              learn/understand. We're also very comfortable with Python and the 
              availability of official python drivers (also JavaScript & Ruby, and a 
              heap for user contributed for a swag of languages) is a big bonus.
        
        
        BanzaiDB Requirements
        ---------------------
        
        You will need:
            * (probably) administrator access to your machine(s)
            * a RethinkDB_ server/instance. This can be running locally or on a VPS, 
            * git (to clone this repository) and
            * pip_
        
        You will also need a few Python modules:
            * rethinkdb
            * biopython
            * reportlab
            * fabric
            * tablib
            * argparse (if Python 2.6)
        
        The Python modules should/will be pulled down automatically when installing 
        BanzaiDB.
        
        We recommend you increase the rethinkdb python `driver performance`_. We have 
        found that in some cases the installation of C++ backend fails. `We provide`_ 
        a simple protocol that we have found works.
        
        
        BanzaiDB Installation
        ---------------------
        
        Something like this::
        
            $ git clone https://github.com/mscook/BanzaiDB.git
            $ cd BanzaiDB
            $ python setup.py install
        
        
        Getting BanzaiDB talking to RethinkDB
        -------------------------------------
        
        You provide information about you RethinkDB instance and database using the 
        file **~/.BanzaiDB.cfg** (~/ is shorthand for $HOME).
        
        The configuration file supports::
        
            db_host  =  [def = localhost]
            port     =  [def = 28015]
            db_name  =  [def = Banzai]
            auth_key =  [def = '']
        
        
        BanzaiDB usage
        --------------
        
        **Note:** Please refer to the `BanzaiDB documentation`_ (via ReadTheDocs) for 
        more detailed information (under active development).
        
        Once both RethinkDB and BanzaiDB are installed and the configuration is set::
        
            $ python BanzaiDB.py -h
            usage: BanzaiDB.py [-h] [-v] {init,populate,update,query} ...
        
            BanzaiDB v 0.1.2 - Database for Banzai NGS pipeline tool
            (http://github.com/mscook/BanzaiDB)
        
            positional arguments:
              {init,populate,update,query}
                                    Available commands:
                init                Initialise a DB
                populate            Populates a database with results of an experiment
                update              Updates a database with results from a new experiment
                query               List available or provide database query functions
        
            optional arguments:
              -h, --help            show this help message and exit
              -v, --verbose         verbose output
        
            Licence: ECL 2.0 by Mitchell Stanton-Cook <m.stantoncook@gmail.com>
        
        
        
        .. _RethinkDB: http://www.rethinkdb.com
        .. _NoSQL: http://nosql-database.org
        .. _Banzai NGS pipeline: https://github.com/mscook/Banzai-MicrobialGenomics-Pipeline
        .. _BanzaiDB documentation: http://banzaidb.readthedocs.org
        .. _driver performance: http://www.rethinkdb.com/docs/driver-performance/
        .. _pip: http://pip.readthedocs.org/en/latest/installing.html
        .. _We provide: https://raw.githubusercontent.com/mscook/BanzaiDB/master/misc/python_C++_driver.sh
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 2 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
