kristiyanto/biodepot-workflow-builder repository overview

⁠BioDepot Workflow Builder (BwB)

BioDepot is a self-contained tool with graphical user interface for bioinformatic workflows. The package is based on Orange 3 by Biolab and NoVnc. Widgets are mainly written in Python (Qt5, Docker-Py, PyQt5).

⁠Requirements

• Docker 1.13.0 or above
• Internet Browser

⁠Running BwB

Currently, BwB uses docker sock binding, to run BwB:

1. Install Docker
2. On Docker-enabled machines run:

docker pull biodepot/bwb:latest
docker run -p 6080:6080 -v ${PWD}:/data -v /var/run/docker.sock:/var/run/docker.sock biodepot/bwb

1. BwB can be accessed from browser: http://localhost:6080⁠ (if you're running it on the cloud, replace localhost with your cloud address.)

⁠Sample Workflows

Some sample workflows are available:

1. Adaptation of Michael Love's et al. Aligment at Gene Level Alignment⁠. Alignment (STAR), Count matrix computation, differential gene analyses (DESeq).
2. DToxS RNA-Seq: Burroughs-Wheeler Aligner for alignment and EdgeR for differential gene expression.⁠
3. More sample workflows.⁠

⁠Developing Widget

To add a widget to BioDepot:

1. Download BioDepot source codes:
 https://github.com/BioDepot/BioDepot-workflow-builder/tree/master/biodepot 

2. Locate to folder orangebiodepot (eg: ~/Desktop/biodepot/orangebiodepot)

3. Write the widget (or copy any of existing widgets and modify as necessary)

4. On BwB, run xterm and locate to the shared widget location (e.g: /data/biodepot)

5. Rebuild BioDepot and rerun Orange:

    pip3 uninstall BioDepot
    pip3 install -e .
    orange-canvas

⁠More resources:

• Demo: Link⁠
• Manual: Manual⁠