Load Genome Script: Difference between revisions
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* fasta_files | * fasta_files | ||
** comma-separated list of FASTA files | ** comma-separated list of FASTA files | ||
* staging_dir temporary staging directory for processing files, use "." | * staging_dir | ||
* install_dir permanent installation directory for genome files with DATADIR in configuration file | ** temporary staging directory for processing files, use "." | ||
* user_id user ID | * install_dir | ||
* config | ** permanent installation directory for genome files with DATADIR in configuration file | ||
* user_id | |||
** user ID | |||
* config | |||
** configuration file | |||
Optional parameters: | Optional parameters: | ||
Revision as of 17:32, 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