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A plugin for PathMe that allows to explore overlaps across pathway databases.

Project description

This plugin initializes the pathway viewer in ComPath that allows to explore overlaps between pathways using the canonical mappings.

Installation Current version on PyPI Stable Supported Python Versions Apache-2.0

  1. pathme_viewer can be installed with the following commands:

$ python3 -m pip install git+https://github.com/ComPath/PathMe-Viewer.git@master
  1. or in editable mode with:

$ git clone https://github.com/ComPath/PathMe-Viewer.git
$ cd PathMe-Viewer
$ python3 -m pip install -e .

Database

The web application requires to load the pathways from the databases in the BEL. Thus, it is required to the following command to load the database (note that the first time it runs might take a couple of hours).

python3 -m pathme_viewer manage load

In order to check the status of the database, you can run:

python3 -m pathme_viewer manage summarize

The content of the database can be erased by running:

python3 -m pathme_viewer manage drop

Deployment

Once the desired pathway databases are loaded, you can deploy the web application by running:

python3 -m pip install pathme_viewer web

Note that the database runs by default in the following port: http://0.0.0.0:5000/. The Flask host and port can be modified by changing the default parameters (run: “python3 -m pathme_viewer web –help” for more info).

Deployment of ComPath with Docker

Note: the docker file is meant to be run on 0.0.0.0:5000. If you want to change the host/port please modify dockerfile (line 55) and src/bin/bootstrap.sh (line 23).

  1. Build the container named ‘pathme’ version 0.0.1.

docker build -t pathme:0.0.1 .
  1. Run docker the pathme container version 0.0.1.

docker run --name=pathme -d -p 5000:5000 --restart=always -d pathme:0.0.1

How to Use

Here is an example of the visualization of Apoptosis equivalent pathways.

https://github.com/ComPath/PathMe-Viewer/blob/master/src/pathme_viewer/static/img/visualization_example.png

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