Load Genome Script: Difference between revisions
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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 17:31, 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