MetaKeggWeb

Web interface for https://github.com/dife-bioinformatics/metaKEGG

Authors: Justus Täger DZD, Tim Bleimehl DZD

• MetaKeggWeb
• Install and Run
  • Option1: Run with prebuild container
    • Download
    • Run
    • Usage
  • Option2: Build and run with Docker
    • Download
    • Building
    • Start
    • Usage
  • Option3: Build and run locally
    • Download
    • Build Server
    • Build Client
    • Start
    • Usage
• Configuration
  • Via environment Variable
  • Via Yaml file
    • Local
    • Docker
• Notes on running in production

Install and Run

Important

This project is intended to run in a Linux/Unix environment. It should also be able to run in a MS Windows environment but was not tested yet. There may be are still bugs regarding Path resolutions on MS Windows.

Option1: Run with prebuild container

Download

docker pull dzdde/metakeggweb

Run

docker run -p 8282:8282 dzdde/metakeggweb

Usage

visit http://localhost:8282 to use the MetaKegg WebClient

visit http://localhost:8282/docs to see the OpenAPI Rest Specification

Option2: Build and run with Docker

requirements

• git for downloading the project
  • https://www.python.org/downloads/
• docker For building and running the project
  • https://docs.docker.com/engine/install/

Download

git clone git@github.com:DZD-eV-Diabetes-Research/meta-kegg-web-wrapper.git

cd meta-kegg-web-wrapper

Building

docker build . -t metakeggweb

Start

docker run -p 8282:8282 metakeggweb

Usage

visit http://localhost:8282 to use the MetaKegg WebClient

visit http://localhost:8282/docs to see the OpenAPI Rest Specification

Option3: Build and run locally

requirements

• git for downloading the project
  • https://www.python.org/downloads/
• python >= v.3.11 for building and running the server
  • https://www.python.org/downloads/
• bun for building the Webclient
  • https://bun.sh/docs/installation

Download

git clone git@github.com:DZD-eV-Diabetes-Research/meta-kegg-web-wrapper.git

cd meta-kegg-web-wrapper

Build Server

python -m pip install -r ./backend/requirements.txt -U

There are some mandatory config setting we need to set. create a .env file at backend/mekeweserver/.env Write this content into the file backend/mekeweserver/.env

SERVER_HOSTNAME=localhost

Build Client

Download and install depencencies for client

(cd frontend && bun install)

Build static pages for the client

(cd frontend && bunx nuxi generate)

Start

Finally we can start the MetaKegg Webserver with:

python backend/mekeweserver/main.py

Usage

visit http://localhost:8282 to use the MetaKegg WebClient

visit http://localhost:8282/docs to see the OpenAPI Rest Specification

Configuration

MetaKegg has a range of configuration variables. Most are set to sane default values.

Have a look at config.template.yaml to see a template with all possible configuration parameters.

Via environment Variable

You can set any configuration variable via env vars. This is convenient via Docker

For example lets define the log level in our instance.

docker run -p 8282:8282 -e LOG_LEVEL=INFO metakeggweb

Via Yaml file

If you want to MetaKeggWeb to use a custamized config yaml file, set the environment variabel MEKEWESERVER_YAML_CONFIG_FILE with a path pointing to your yaml.

Lets create a config yaml first

/tmp/config.yaml

LOG_LEVEL: INFO
PIPELINE_RUNS_CACHE_DIR: /tmp/mekewe_cache

Local

Now we want to set MEKEWESERVER_YAML_CONFIG_FILE to point to our yaml file

On MS Windows: set MEKEWESERVER_YAML_CONFIG_FILE="C:\tmp\config.yaml"

On *nix: export MEKEWESERVER_YAML_CONFIG_FILE="/tmp/config.yaml"

If we now start our webserver with
python backend/mekeweserver/main.py
Our config.yaml will be taken into account.

Docker

With docker we only need to mount our config.yaml into the config directory.

docker run -p 8282:8282 -v /tmp/config.yaml:/config/config.yaml metakeggweb

Notes on running in production

MetaKeggWeb uses a Redis server for interprocess communication.
If no Redis server is provided, the Webserver will run an instance of fakeredis. This is fine for running a local demo.

For a productive instance you should attach a real Redis instance to the server. Have a look at our docker-compose.yaml reference file to see how to do it.