intro.md

Databases

The database used by the website for Guidescan is a PostgreSQL DB. The database stores various bits of genomic information such as gene symbol names, coordinates, and corresponding genomic elements. There are various scripts for these different use cases. Each use case is described below seperately.

The only mandatory component of the database is its schema. This can be created from scratch with the create_gene_db target and is required before running any of the other scripts.

Scripts

To compile the scripts for database database generation, simply run:

$ lein with-profile database-generation uberjar

This will create a bundled jar containing all of the scripts required for various database maintenance and generation tasks.

There are several different tasks supported:

• Database schema creation
  • create_gene_db target
  • instructions here
• Updating the gene database with new organisms
  • add_organism target
  • instructions here
• Adding gRNA libraries
  • add_grna_lib target
  • instructions here