Package: regulome-web
![](https://bitbucket.org/batterio/regulome_web/raw/master/regulome_app/webapp/static/images/regulome_logo.jpg)This repository contains the code of the Islet Regulome Browser.The Islet Regulome Browser is a visualization tool that enables viewingof human islet TF bindings, human islet open chromatin states, clustersof enhancers, islet motifs, and DIAGRAM type2 diabetes associationp-values as well as MAGIC fasting glycemia p-values at desired levels ofresolution throughout the genome. In addition to these standard tracks,it is also possible for users to upload their own variants or regionssets 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 sourcesSince the data sources are large files (~ 8Gb) contact the author (info@isletregulome.com) to download them.## How to install the regulomeThe regulome browser can be installed with various approaches:### Through PyPI (recommended)pip install regulome_web### Through the source packagepip install regulome_web-2.0.tar.gzPut, 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_webFirst, 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 aswell as a `regulome.cfg` configuration file. Configure the configurationfile 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 theregulome_web with a web service such as Apache, use the `regulome.wsgi`file instead. In order to be used in production the regulome_web shouldbe configured with a secure `secret_key` (to be set in the `regulome.cfg`configuration file) and the `deploy_mode` section of the `regulome.cfg` fileshould be set to `production`.## Description of the `regulome.cfg` configuration fileThe `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.