regulome-web 2.0rc2

Human Islet Regulome Browser

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 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

• ImageMagick

Islet regulome data sources

Since the data sources are large files (~ 8Gb) contact the author ([e-mail]) 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 [e-mail]: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.