Illumina Sequencing Instruments Tracking

Currently supported instrument types: NovaSeqX, NovaSeq, HiSeq, MiSeq.

Top Level Directories

• lib - Perl modules and classes
  • npg:: - web application
  • npg_tracking::
    • general definitions
    • access to genomic references and other reference data
    • API for extended Illumina rundolder structure
  • npg_tracking::Schema - DBIx binding for the tracking database
  • st::api:: - LIMS API
  • Monitor:: - monitoring runfolders on staging servers up to the analysis stage
  • npg_testing:: - supplimentary modules for testing
• bin - production Perl scripts
• cgi-bin - cgi scripts for the web application
• scripts - supplimentary scripts
• htdocs - images and client-side scripts for the web application
• data
  • templates for the web app and some cron jobs
  • example database configuration file for the web application
• docs - directory for documentation
• wtsi_local - Apache httpd web server configuration files
• t - unit tests, test data, supplimentary scripts and modules for testing

Environment Variables and Their Meaning

• NPG_CACHED_SAMPLESHEET_FILE - a path to a file with cached LIMS data, see st::api::lims

Tags and Their Meaning

Run and lane tags are described here

Runs Lifecycle

Run statuses are explained here

Sequencing Instrument Lifecycle and Management

See code snippets for creating and updating database records for instruments.

User Management

Users may ask to get some permissions to create new runs in the tracking system. To grant permissions the User Management guide explains how to assign the users to different groups.