PLEASE NOTE THAT THE PROJECT MOVED TO https://github.com/panoptes-organization/panoptes/

panoptes

Bioinformaticians and data scientists, rely on computational frameworks (e.g. snakemake, nextflow, CWL, WDL) to process, analyze and integrate data of various types. Such frameworks allow scientists to combine software and custom tools of different origin in a unified way, which lets them reproduce the results of others, or reuse the same pipeline on different datasets. One of the fundamental issues is that the majority of the users execute multiple pipelines at the same time, or execute a multistep pipeline for a big number of datasets, or both, making it hard to track the execution of the individual steps or monitor which of the processed datasets are complete. panoptes is a tool that monitors the execution of such workflows.

panoptes is a service that can be used by:

• Administrations that want to monitor their servers
• Data scientists, bioinformaticians, etc. that want to have a general overview of the progress of their pipelines
• Web developers that want to integrate the service in bigger web applications

Note: panoptes is in early development stage and the first proof of concept server will support only workflows written in snakemake.

Installation

Development installation

Requirements

• Python>=3.6
• sqlite3
• npm

Install sqlite3

Install sqlite3

Install server

Clone repo

git clone -b develop https://github.com/fgypas/panoptes.git

Enter repo

cd panoptes

Create virtual environment

virtualenv -p `which python3` venv

Create virtual environment

source venv/bin/activate

Install requirements

pip install -r requirements.txt

Enter coreui directory and install javascipt dependencies

cd server/static
npm install

Go to the root directory

cd ../../

EXPORT FLASK_APP

export FLASK_APP=server/app.py
export FLASK_ENV=development

Run server

python -m flask run

Server should run on: http://127.0.0.1:5000/

Contribute

Please see the Contributing instructions.