Difference between revisions of "Load Genome Script"
From CoGepedia
| Line 7: | Line 7: | ||
Required parameters: | Required parameters: | ||
| − | + | * fasta_files comma-separated list of 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 | + | * user_id user ID |
| − | user_id user ID | + | * config configuration file |
| − | config configuration file | + | |
| − | + | ||
Optional parameters: | Optional parameters: | ||
| − | + | * name String name of the genome | |
| − | name String name of the genome | + | * desc String description of the genome |
| − | desc String description of the genome | + | * link URL to the data source or publication |
| − | link URL to the data source or publication | + | * version Version of the genome data |
| − | version Version of the genome data | + | * type_id Sequence type ID, defaults to 1 for "unmasked" |
| − | type_id Sequence type ID, defaults to 1 for "unmasked" | + | * restricted Flag to make genome private (1) or public (0) |
| − | restricted Flag to make genome private (1) or public (0) | + | * organism_id Organism ID |
| − | organism_id Organism ID | + | * source_name Name of data source, e.g. the lab that generated the sequence data |
| − | source_name Name of data source, e.g. the lab that generated the sequence data | + | * source_desc Description of the data source |
| − | source_desc Description of the data source | + | |
| − | + | ||
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
