Load Genome Script

The load genome script, load_genome.pl, allows genomes to be created via the backend.

Usage:

perl load_genome.pl -name <string> -desc <string> ...

Required parameters:

• fasta_files comma-separated list of FASTA files
• staging_dir temporary staging directory for processing files, use "."
• install_dir permanent installation directory for genome files with DATADIR in configuration file
• user_id user ID
• config configuration file

Optional parameters:

• name String name of the genome
• desc String description of the genome
• link URL to the data source or publication
• version Version of the genome data
• type_id Sequence type ID, defaults to 1 for "unmasked"
• restricted Flag to make genome private (1) or public (0)
• organism_id Organism ID
• source_name Name of data source, e.g. the lab that generated the sequence data
• source_desc Description of the data source