A web application for exploring and comparing the overlaps across pathway resources
Project description
An integrative and extensible web application for exploring, analyzing, and curating pathway databases.
This package exposes the Bio2BEL pathway packages into a web application containing multiple built-in visualization and analytics tools allowing for their analysis and comparison. By default, this packages wraps the following default packages:
New pathway/gene signatures resources can be added by forking the ComPath Template Repository.
Installation 
compath can be installed easily from PyPI with the following code in your favorite terminal:
python3 -m pip install compathor from the latest code on GitHub with:
python3 -m pip install git+https://github.com/bio2bel/compath.git@masterSetup
Easiest
After installing compath, run from the command line:
python3 -m compath populateThis command populates all of the relevant Bio2BEL repositories for the default list, and if any optional ComPath repositories have been registered with entry points, will also populated.
For Developers
If you just cloned the repo and installed it from the source code, you can run the sh script load_compath.sh by
typing sh load_compath.sh in your terminal. This script will first install all packages and later populate the
database.
If you have already installed the packages, but not loaded the data. First, load
Bio2BEL HGNC (see ‘Mapping across gene/protein identifiers’ section). Next, load all individual pathway database
packages KEGG, Reactome, WikiPathways, and MSigDB with python3 -m compath populate. This command assumes that
these packages are already installed in your Python environment. You can check the packages installed by running
python3 -m compath ls in your terminal. Alternatively, you can populate each package independently by running:
python3 -m bio2bel_kegg populate, python3 -m bio2bel_reactome populate,
python3 -m bio2bel_wikipathways populate, or python3 -m bio2bel_msig 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:
python3 -m pip install bio2bel_hgncpython3 -m bio2bel_hgnc populate
Running the Web Application
The application can be run simply with
python3 -m compath webThis 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_mappingsLoad hierarchical mappings from a pathway database already containing that information (e.g., Reactome).
python3 -m compath load_hierarchiesCreate 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'Docker Instructions
Build Docker Image
docker build -t compath:0.0.1 .Create Docker Containers
sh create_and_build_container.shStart Docker execution container
docker run --name=compath --volumes-from compath-data --restart=always -d -p 30050:5000 docker.arty.scai.fraunhofer.de/compath:latestLoad Data
docker exec -t -it compath /opt/compath/src/bin/load_data.shRestart Container
docker restart compath
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