BiSePS: Bisulfite Sequencing Processing

BiSePS is a desktop application for analyzing Whole Genome Bisulfite Sequencing data. It's a Mongodb/express/React/Nodejs app bundled with webpack and packaged into a desktop app using Electron. It runs a snakemake pipeline under the hood for processing data locally or on remote machines using ssh credentials. It relies on git and conda for workflow retrieval and dependencies management. It also supports SLURM cluster execution.

Use this app along with the BiSePS documentation for configuration examples to help you get started.

Dependencies

For BiSePS to run you need these dependencies installed on your machine.

• conda - miniconda for package management.
• git - git to get latest release of the workflow.
• nodejs - node to build the gui.

To Use

To use this app you can either download executables from the releases page. Or build it on your machine from the command line:

# Clone this repository
git clone https://forgemia.inra.fr/irhs-bioinfo/bisepsgui.git
# Go into the repository
cd bisepsgui

Install nodejs version 16 using nvm:

# Install nvm
wget -qO- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.3/install.sh | bash
nvm install 16
nvm use 16

Install yarn:

# Install yarn using corepack
corepack enable
corepack prepare yarn@stable --activate

Next, install dependencies with yarn:

# Install Electron dependencies
yarn
# Go into the backend folder
cd src/backend
# Install dependencies
yarn

Then start the app:

# Go into repository folder
cd ../../
# Start application
yarn start

To Build

Linux

sudo apt update -y
sudo apt install -y cmake rpm fakeroot dpkg
yarn make

Windows/Macos

yarn make

Resulting files are in out/make/

References

• BiSePS Workflow
• Snakemake
• Bismark
• Methylkit
• Bedtools
• MultiQC
• FastQC
• MethGet
• Jbrowse2

License

MIT