Streamlit-HGB

A streamlit component for a hybrid genome browser

• virtualenv

$ python3 -m venv venv  # create venv
$ . venv/bin/activate   # activate venv
$ pip install streamlit # install streamlit
$ pip install pyyaml    # install pyyaml

• frontend

$ cd hgb/frontend
$ npm install    # Initialize the project and install npm dependencies
$ npm run start  # Start the Webpack dev server

• backend

export STREAMLIT_HOST=$(hostname -i)
export HGB_BIN=/*location_to_hgb_binary*/

streamlit run hgb/__init__.py 

Demo Example

https://github.com/6br/hgb_demo

Example of config.yaml

hg38:
  range: 
    - chr1:1-1000001
  default:
    - "/path/to/bamfile1.bam"
  samples: 
    - "/path/to/bamfile1.bam"
    - "/path/to/bamfile2.bam"

• Range: a default range to visualize
• Default: a default set of BAM file to be loaded
• Samples: a list of BAM file

All input bam files must be indexed by samtools index or compatibles.