genomes

This section is auto-generated from the help text for the parsec command genomes.

get_genomes command

Usage:

parsec genomes get_genomes [OPTIONS]

Help

Returns a list of installed genomes

Output

Options:

-h, --help  Show this message and exit.

install_genome command

Usage:

parsec genomes install_genome [OPTIONS]

Help

Download and/or index a genome.

Output

dict( status: ‘ok’, job: <job ID> )

If error: dict( status: ‘error’, error: <error message> )

Options:

--func TEXT           Allowed values: 'download', Download and index; 'index',
                      Index only  [default: download]
--source TEXT         Data source for this build. Can be: UCSC, Ensembl, NCBI,
                      URL
--dbkey TEXT          DB key of the build to download, ignored unless 'UCSC'
                      is specified as the source
--ncbi_name TEXT      NCBI's genome identifier, ignored unless NCBI is
                      specified as the source
--ensembl_dbkey TEXT  Ensembl's genome identifier, ignored unless Ensembl is
                      specified as the source
--url_dbkey TEXT      DB key to use for this build, ignored unless URL is
                      specified as the source
--indexers TEXT       POST array of indexers to run after downloading
                      (indexers[] = first, indexers[] = second, ...)
-h, --help            Show this message and exit.

show_genome command

Usage:

parsec genomes show_genome [OPTIONS] ID

Help

Returns information about build <id>

Output

Options:

--num TEXT    num
--chrom TEXT  chrom
--low TEXT    low
--high TEXT   high
-h, --help    Show this message and exit.