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, 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 | ||
** comma-separated list of FASTA files | ** comma-separated list of FASTA files | ||
* staging_dir temporary staging directory for processing files, use "." | * staging_dir | ||
* install_dir permanent installation directory for genome files | ** temporary staging directory for processing files, use "." | ||
* user_id user ID | * install_dir | ||
* config | ** 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 17:57, 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