Difference between revisions of "Load Genome Script"
From CoGepedia
| Line 7: | Line 7: | ||
Required parameters: | Required parameters: | ||
| − | * fasta_files | + | * fasta_files |
| + | ** comma-separated list of FASTA files | ||
* staging_dir temporary staging directory for processing files, use "." | * staging_dir temporary staging directory for processing files, use "." | ||
* install_dir permanent installation directory for genome files with DATADIR in configuration file | * install_dir permanent installation directory for genome files with DATADIR in configuration file | ||
Revision as of 10:31, 16 February 2015
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
