Metadata-Version: 2.0
Name: regulome-web
Version: 2.0.0rc3
Summary: Human Islet Regulome Browser
Home-page: https://bitbucket.org/batterio/regulome_web
Author: Loris Mularoni
Author-email: loris@mularoni.com
License: MIT License
Download-URL: https://bitbucket.org/batterio/regulome_web/get/2.0.0rc3.tar.gz
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: Flask
Requires-Dist: Jinja2
Requires-Dist: Click

.. figure:: https://bitbucket.org/batterio/regulome_web/raw/master/regulome_app/webapp/static/images/regulome_logo.jpg
   :alt: 

This repository contains the code of the Islet Regulome Browser. The
Islet Regulome Browser is a visualization tool that enables viewing of
human islet TF bindings, human islet open chromatin states, clusters of
enhancers, islet motifs, and DIAGRAM type2 diabetes association p-values
as well as MAGIC fasting glycemia p-values at desired levels of
resolution throughout the genome. In addition to these standard tracks,
it is also possible for users to upload their own variants or regions
sets for temporary display.

Islet regulome dependencies
---------------------------

-  `Python 3.5 <https://www.python.org/>`__ and newer with the following
   packages:

   -  Flask
   -  Click
   -  pandoc (optional)
   -  Optional modules that will probably be used in the future are:

      -  intervaltree
      -  SQLAlchemy
      -  Flask-SQLAlchemy
      -  matplotlib

-  `R <https://www.r-project.org/>`__
-  `ImageMagick <http://www.imagemagick.org/>`__

Islet regulome data sources
---------------------------

Since the data sources are large files (~ 8Gb) contact the author
(info@isletregulome.com) to download them.

How to install the regulome
---------------------------

The regulome browser can be installed with various approaches:

Through PyPI (recommended)
~~~~~~~~~~~~~~~~~~~~~~~~~~

::

    pip install regulome_web  

Through the source package
~~~~~~~~~~~~~~~~~~~~~~~~~~

::

    pip install regulome_web-2.0.tar.gz  

Put, if necessary, the correct version of the program in the name of the
package

By cloning the repository:
~~~~~~~~~~~~~~~~~~~~~~~~~~

-  Clone the regulome repository:
   ``git clone git@bitbucket.org:batterio/regulome_web.git``
-  Install the package:
   ``pip install -e .``
   *or*
   ``python setup.py``

How to run the regulome\_web
----------------------------

First, install the regulome\_web as described above. Then write
``regulome_web --help`` to obtain some basic information about the usage
of the regulome\_web. Once the package is installed, create the required
structure by executing ``regulome_web init``. This command will create a
structure of folders as well as a ``regulome.cfg`` configuration file.
Configure the configuration file and then run the regulome\_web by
executing ``regulome_web start``. This will start a local web server on
``http://127.0.0.1:5000/``. To deploy the regulome\_web with a web
service such as Apache, use the ``regulome.wsgi`` file instead. In order
to be used in production the regulome\_web should be configured with a
secure ``secret_key`` (to be set in the ``regulome.cfg`` configuration
file) and the ``deploy_mode`` section of the ``regulome.cfg`` file
should be set to ``production``.

Description of the ``regulome.cfg`` configuration file
------------------------------------------------------

The ``regulome.cfg`` configuration file is composed of 7 fields, denoted
by square brackets:

-  **binaries**: contains two variables:

   -  **Rscript\_bin**: path of the R binary
   -  **imagemagick**: path of the imagemagick convert tool

-  **working\_directory**: contains one variable:

   -  **cwd**: current working directory. This field is set
      automatically by the program when ``regulome_web init`` is
      executed

-  **data**: contains two variables:

   -  **data**: path of the data used by the R script to generate the
      plot. By default the program searches for the folder ``data`` in
      the current working directory (see above)
   -  **uploads**: path where the files uploaded by the users are
      stored. By default the program searches for the folder
      ``data/uploads`` in the current working directory (see above)

-  **output**: contains one variable:

   -  **cache**: path where the results of the program (plots and
      tables) will be saved. By default the program searches for the
      folder ``output`` in the current working directory (see above).
      The default folder will be created, if not existing, when
      ``regulome_web init`` is executed

-  **logs**: contains 4 variables:

   -  **log\_folder**: path where the logs of the program are written.
      By default the program searches for the folder ``logs`` in the
      current woring directory (seea bove). The default folder will be
      created, if not existing, when ``regulome_web init`` is executed
   -  **activity\_log**: path of the ``activity.log`` file. By default
      this file is placed inside ``log_folder``
   -  **regulome\_log**: path of the ``regulome.log`` file. By default
      this file is placed inside ``log_folder``
   -  **log\_level**: level of log verbosity: can be: notset, debug,
      info, warning, error, critical. By default log\_level is set to
      info

-  **deploy\_mode**: contains one variable:

   -  **configuration**: mode of deploy of the ``regulome_web`` program.
      Can be development, testing, production. By default cofiguration
      is set to development

-  **secret\_key**: contains one variable:

   -  **key**: key used to encrypt the session coockies. Make sure to
      keep the key secret.


