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chembl_beaker 0.2.3

RDKit in the Bottle on Tornado

Latest Version: 1.0.0

chembl_beaker
======

What is Beaker?
--------

This is chembl_beaker package developed at `Chembl <https: www.ebi.ac.uk="" chembl=""/>`_ group, `EMBL-EBI <https: www.ebi.ac.uk=""/>`_, Cambridge, UK.

This is wrapper for `RDKit <http: www.rdkit.org=""/>`_ and `OSRA <http: cactus.nci.nih.gov="" osra=""/>`_, which exposes following RDKit functions:

* Format convertion
* Fingerprints
* Descriptors

As a portable lightweight webserver, speaking REST. This particular implementation wraps RDKit in `Bottle <http: bottlepy.org="" docs="" dev=""/>`_ on `Tornado <http: www.tornadoweb.org="" en="" stable=""/>`_.

Where is it used?
--------

Beaker is used in `Clippy <https: github.com="" madgpap="" chembl_clippy="">`_ project but can be used as a standalone web server as well.

Software dependencies
--------

* `RDKit <http: www.rdkit.org=""/>`_
* `OSRA <http: cactus.nci.nih.gov="" osra=""/>`_
* `Bottle <http: bottlepy.org="" docs="" dev=""/>`_
* `Tornado <http: www.tornadoweb.org="" en="" stable=""/>`_

Configuration
--------
By default configuration is stored in ``beaker.conf`` file, located in current directory. You can specify location of
configuration file using ``--config (-c)`` parameter when running beaker. Configuration file format is standard ``*.ini``.
Beaker is distributed with example configuration file named ``beaker.conf.sample``.

* **debug** - run bottle server in debug mode (True/False, default ``True``)
* **bottle_port** - number of porn on which Bottle server is listening for connections (integer, default ``8080``)
* **bottle_host** - hostname of Bottle server (string, default ``localhost``)
* **server_middleware** - networking middleware library used by Bottle (string, default ``tornado``)
* **osra_binaries_location** - path to OSRA binary you want to use for compound recognition (string, default ``/usr/bin/osra``)

Running
--------
If you want to play with beaker run ``python run_beaker.py``
If you want to run beaker in production you should do this using virtualenv, uWSGI and NGINX as described `here <http: fclef.wordpress.com="" 2013="" 01="" 12="" bottle-virtualenv-uwsgi-nginx-installation-on-ubuntu-12-04-1-lts=""/>`_. Other standard python deployment stacks will work as well.

More info and help
--------

More information can be found in `web based presentation <https: github.com="" mnowotka="" beaker-presentation="">`_. You can always email the author: mmmnow@gmail.com  
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