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Local installation

Run pATLAS locally

You can run pATLAS locally without much requirements by using patlas-compose. This will automatically handle the installation of the version 1.5.2 of pATLAS and launch the service in a local instance. For that you just require:
Then, follow this simple steps:
git clone https://github.com/bfrgoncalves/patlas-compose
  • Enter the patlas-compose folder
cd patlas-compose
  • Launch the compose:
docker-compose up
  • Wait for the line * Running on http://0.0.0.0:5000/ (Press CTRL+C to quit) to show up, meaning that the service is now running.
  • Access on 127.0.0.1:5000 or 0.0.0.0:5000.

From scratch (alternatively)

pATLAS can be run locally if you have PostgreSQL installed and configured. After, you just need to:
1) Clone this repository:
git clone https://github.com/tiagofilipe12/pATLAS
2) Create your custom database version or generate the default pATLAS database or download sql file from version 1.6.1 (the tar.gz archive). Note: if you download the sql file from version 1.6.1 you may skip steps 3 to 4 and continue with step 5.
3) Make sure all the necessary files are in place.
  • by default pATLAS generates a import_to_vivagraph.json file in
    the folder <tag_provided_to_o_flag>/results. Place this file in the
    patlas/db_manager/db_app/static/json folder.
  • change session to read the new import_to_vivagraph.json file by
    changing from false to true a variable named devel in
    patlas/db_manager/db_app/static/js/pATLASGlobals.js
4) Create the database that the front end will run:
createdb <your_database>
6) Install backend dependencies:
# within the root directory of this repository
pip install -r requirements.txt
7) Install frontend dependencies:
# change directory to static direcoty where `index.html` will look for
# its depdendenies
cd patlas/db_manager/db_app/static/
# then install them (package.json is located in this directory)
yarn install
8) Compile node modules so that the html can understand, using webpack:
# You can also user a local installation of webpack.
# entry-point.js is the config file where all the imported modules are
# called
node_modules/webpack/bin/webpack.js entry-point.js
9) Then execute the script run.py.
# within the root directory of this repository
cd patlas/db_manager
./run.py <your_database>
Note: the database name is utterly important to properly say to the frontend where to get the data.
10) Go to 127.0.0.1:5000.

Optimization of the resources usage by the web page

Using the devel = true isn't very efficient, so you can allow the force directed graph to render in a devel = true session, then when you are satisfied pause the force layout using the buttons available in pATLAS and click at the same time Shift+Ctrl+Space. This will take a while but eventually it will generate a file named filtered.json. Once you have this file you can add it to the patlas/db_manager/db_app/static/json folder and change the devel variable to false. This will use the previously saved positions to render a pre rendered network.
Last modified 4yr ago
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On this page
Run pATLAS locally
Docker compose (recommended)
From scratch (alternatively)
Optimization of the resources usage by the web page