compath 0.1.0

Installation

compath can be installed easily from PyPI with the following code in your favorite terminal:

python3 -m pip install compath

or from the latest code on GitHub with:

python3 -m pip install git+https://github.com/bio2bel/compath.git@master

Setup

python3 -m compath populate

Mapping across gene/protein identifiers

In order to load the gene sets from default packages, ComPath assumes that Bio2BEL HGNC has been already installed and populated. This package is required to perform the mapping from multiple Protein/Gene identifiers to HGNC symbols. The following steps are needed to install Bio2BEL HGNC:

1. python3 -m pip install bio2bel_hgnc

2. python3 -m bio2bel_hgnc populate

Running the Web Application

The application can be run simply with

python3 -m compath web

This command the Flask development server locally, by default on port 5000 (http://localhost:5000).

Curation Interface

Load mappings between pathways directly from the ComPath Curation package.

python3 -m compath load_mappings

Load hierarchical mappings from a pathway database already containing that information (e.g., Reactome).

python3 -m compath load_hierarchies

Create a user.

python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_user  'email' 'password'

Make user admin.

python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_admin 'email'

Build Docker Image

docker build -t compath:0.0.1 .

Create Docker Containers

sh create_and_build_container.sh

Start Docker execution container

docker run --name=compath --volumes-from compath-data --restart=always -d -p 30050:5000 docker.arty.scai.fraunhofer.de/compath:latest

Load Data

docker exec -t -it compath /opt/compath/src/bin/load_data.sh

Restart Container

docker restart compath