GST is a tool for tracking and visualizing genomics sample processing data. It provides functionality to export sample data to TSV files and serves an interactive web dashboard for data exploration.
GST requires a .env
file in the root directory with the following variables:
GST_SQL_USER=gst_reader
GST_SQL_PASS=secret_password
GST_SQL_HOST=mysql.example.com
GST_SQL_PORT=3306
GST_SQL_DB=sample_tracking
go install
GST provides two main subcommands: export and server.
Exports sample data to a TSV file.
gst export --output samples.tsv
# Start the server with default settings (port 8080)
gst server
# Specify a custom port
gst server --port 3000
# Use mock data instead of querying the database
gst server --mock samples.tsv
After starting the server, open your web browser and navigate to:
The web dashboard provides:
- A tabular view of all sample data with key information
- A stacked horizontal bar chart showing Library Time and Sequencing Time for each sample
The chart is interactive - hover over bars to see detailed information about each sample.
- The database query may take several minutes to complete
- For testing purposes, use the --mock flag with a sample TSV file