Load Genome Script: Difference between revisions

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

@@ Line 1: / Line 1: @@
-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>
-perl load_genome.pl -name <string> -desc <string> ...
+perl load_genome.pl -name <string> -desc <string> -fasta_files <file1>,<file2>,...<fileN> ...
 </pre>
-Required parameters:
+'''Required parameters:'''
-<pre>
+* 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 with DATADIR in configuration file
+** temporary staging directory for processing files, use "."
-user_id         user ID
+* install_dir
-config           configuration file
+** permanent installation directory for genome files
-</pre>
+** 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:'''
-<pre>
+* name
-name                String name of the genome
+** String name of the genome
-desc                 String description of the genome
+* desc
-link                   URL to the data source or publication
+** String description of the genome
-version             Version of the genome data
+* link
-type_id             Sequence type ID, defaults to 1 for "unmasked"
+** URL to the data source or publication
-restricted          Flag to make genome private (1) or public (0)
+* version
-organism_id      Organism ID
+** Version of the genome data
-source_name    Name of data source, e.g. the lab that generated the sequence data
+* type_id
-source_desc     Description of the data source
+** Sequence type ID, defaults to 1 for "unmasked"
-</pre>
+* source_desc
+** Description of the data source
+* restricted
+** Flag to make genome private (1) or public (0), defaults to public

Load Genome Script: Difference between revisions

Latest revision as of 17:57, 16 February 2015

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