Load Genome Script: Difference between revisions
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Created page with 'The load genome script, load_genome.pl, allows genomes to be created via the backend. Usage: <pre> perl load_genome.pl -name <string> -desc <string> ... </pre> Required paramet...' |
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Required parameters: | Required parameters: | ||
fasta_files | <pre> | ||
staging_dir | fasta_files comma-separated list of FASTA files | ||
install_dir | staging_dir temporary staging directory for processing files, use "." | ||
user_id | install_dir permanent installation directory for genome files with DATADIR in configuration file | ||
config | user_id user ID | ||
config configuration file | |||
</pre> | |||
Optional parameters: | Optional parameters: | ||
name | <pre> | ||
desc | name String name of the genome | ||
link | desc String description of the genome | ||
version | link URL to the data source or publication | ||
type_id | version Version of the genome data | ||
restricted | type_id Sequence type ID, defaults to 1 for "unmasked" | ||
organism_id | restricted Flag to make genome private (1) or public (0) | ||
source_name | organism_id Organism ID | ||
source_desc | source_name Name of data source, e.g. the lab that generated the sequence data | ||
source_desc Description of the data source | |||
</pre> | |||
Revision as of 17:30, 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