Difference between revisions of "Load Genome Script"
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| − | The load genome script, load_genome.pl, allows genomes to be created via the backend. | + | The load genome script, scripts/load_genome.pl, allows genomes to be created from FASTA files via the backend. |
| − | Usage: | + | Some data are required to exist in the database prior to running this script: |
| + | * an organism to specify in the organism_id parameter | ||
| + | * a user to specify in the user_id parameter | ||
| + | * a genomic_sequence_type to specify in the type_id parameter | ||
| + | |||
| + | '''Usage:''' | ||
<pre> | <pre> | ||
| − | perl load_genome.pl -name <string> -desc <string> ... | + | perl load_genome.pl -name <string> -desc <string> -fasta_files <file1>,<file2>,...<fileN> ... |
</pre> | </pre> | ||
| − | Required parameters: | + | '''Required parameters:''' |
| − | * fasta_files | + | * fasta_files |
| − | * staging_dir temporary staging directory for processing files, use "." | + | ** comma-separated list of FASTA files |
| − | * install_dir permanent installation directory for genome files | + | * staging_dir |
| − | * user_id user ID | + | ** temporary staging directory for processing files, use "." |
| − | * config | + | * install_dir |
| + | ** permanent installation directory for genome files | ||
| + | ** should match SEQDIR in the configuration file | ||
| + | ** example: /opt/apache2/coge/data/genomic_sequence/ | ||
| + | * user_id | ||
| + | ** ID for user to associate the genome | ||
| + | * organism_id | ||
| + | ** Organism ID | ||
| + | * source_name | ||
| + | ** Name of data source, e.g. the lab that generated the sequence data | ||
| + | * config | ||
| + | ** CoGe configuration file (web/coge.conf) | ||
| − | 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 |
| − | + | * version | |
| − | + | ** Version of the genome data | |
| − | + | * type_id | |
| + | ** Sequence type ID, defaults to 1 for "unmasked" | ||
| + | * source_desc | ||
| + | ** Description of the data source | ||
| + | * restricted | ||
| + | ** Flag to make genome private (1) or public (0), defaults to public | ||
Latest revision as of 10:57, 16 February 2015
The load genome script, scripts/load_genome.pl, allows genomes to be created from FASTA files via the backend.
Some data are required to exist in the database prior to running this script:
- an organism to specify in the organism_id parameter
- a user to specify in the user_id parameter
- a genomic_sequence_type to specify in the type_id parameter
Usage:
perl load_genome.pl -name <string> -desc <string> -fasta_files <file1>,<file2>,...<fileN> ...
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
- should match SEQDIR in the configuration file
- example: /opt/apache2/coge/data/genomic_sequence/
- user_id
- ID for user to associate the genome
- organism_id
- Organism ID
- source_name
- Name of data source, e.g. the lab that generated the sequence data
- config
- CoGe configuration file (web/coge.conf)
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"
- source_desc
- Description of the data source
- restricted
- Flag to make genome private (1) or public (0), defaults to public
