Difference between revisions of "Load Genome Script"
From CoGepedia
m |
|||
| Line 1: | Line 1: | ||
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 10:33, 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
