Load Genome Script

The load genome script, scripts/load_genome.pl, allows genomes to be created from FASTA files via the backend.

Some data are required to exist in the database prior to running this script:

• an organism to specify in the organism_id parameter
• a user to specify in the user_id parameter
• a genomic_sequence_type to specify in the type_id parameter

Usage:

perl load_genome.pl -name <string> -desc <string> -fasta_files <file1>,<file2>,...<fileN> ...

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
  • should match SEQDIR in the configuration file
  • example: /opt/apache2/coge/data/genomic_sequence/
• user_id
  • ID for user to associate the genome
• organism_id
  • Organism ID
• source_name
  • Name of data source, e.g. the lab that generated the sequence data
• config
  • CoGe configuration file (web/coge.conf)

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"
• source_desc
  • Description of the data source
• restricted
  • Flag to make genome private (1) or public (0), defaults to public