Load Genome Script: Difference between revisions
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The load genome script, load_genome.pl, allows genomes to be created via the backend. | The load genome script, load_genome.pl, allows genomes to be created via the backend. | ||
Usage: | '''Usage:''' | ||
<pre> | <pre> | ||
perl load_genome.pl -name <string> -desc <string> ... | perl load_genome.pl -name <string> -desc <string> ... | ||
</pre> | </pre> | ||
Required parameters: | '''Required parameters:''' | ||
* fasta_files | * fasta_files | ||
** comma-separated list of FASTA files | ** comma-separated list of FASTA files | ||
| Line 18: | Line 18: | ||
** configuration file | ** configuration file | ||
Optional parameters: | '''Optional parameters:''' | ||
* name | * name | ||
* desc String description of the genome | ** String name of the genome | ||
* link URL to the data source or publication | * desc | ||
* version Version of the genome data | ** String description of the genome | ||
* type_id Sequence type ID, defaults to 1 for "unmasked" | * link | ||
* restricted Flag to make genome private (1) or public (0) | ** URL to the data source or publication | ||
* organism_id Organism ID | * version | ||
* source_name Name of data source, e.g. the lab that generated the sequence data | ** Version of the genome data | ||
* source_desc Description of the data source | * 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 | |||
Revision as of 17:33, 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