/galaxy_tool

Primary LanguagePython

Rejuve on Galaxy

To run this project

Run the following commmands

Requirements

  • Node and npm
  • Yarn version 1*

*Installation for yarn

npm i --global yarn
npm set version classic
yarn --version
npm i --global yarn

create a virtual machine

virtualenv .venv; . .venv/bin/activate

Activate the virtual environment if it hasn't been already

source .venv/bin/activate

Upgrade pip if needed.

pip install --upgrade pip

Install planemo

Planemo is a set of Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.

pip install planemo

Afterwards to run the server run

 planemo s

Or

planemo serve

Planemo will download and configure a disposable Galaxy instance before running the server if you want to avoid that, clone the following repository

git clone https://github.com/galaxyproject/galaxy

then run

 planemo s --galaxy_root="PATH_TO_GALAXY_REPO"

Or

planemo serve --galaxy_root="PATH_TO_GALAXY_REPO"

Format of nodes and edges expected by the CLI

python script.py --nodes "type1,id1,prop1,prop2" "type2,id2,prop3" --edges "id1,id2,edgeType"