remote

This section is auto-generated from the help text for the arrow command remote.

add_organism command

Usage:

arrow remote add_organism [OPTIONS] COMMON_NAME ORGANISM_DATA

Help

Add an organism using the remote organism API.

Output

a dictionary with information about the new organism

Options:

--blatdb FILENAME               Path to 2bit index of the genome for Blat
                                (Blat 2bit data can also be in organism_data
                                in directory 'searchDatabaseData')

--genus TEXT                    Genus
--species TEXT                  Species
--public                        should the organism be public
--non_default_translation_table INTEGER
                                The translation table number for the organism
                                (if different than that of the server's
                                default)

--metadata TEXT                 JSON formatted arbitrary metadata
-h, --help                      Show this message and exit.

add_track command

Usage:

arrow remote add_track [OPTIONS] ORGANISM_ID TRACK_DATA TRACK_CONFIG

Help

Adds a tarball containing track data to an existing organism.

Output

a dictionary with information about all tracks on the organism

Options:

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

delete_organism command

Usage:

arrow remote delete_organism [OPTIONS] ORGANISM_ID

Help

Remove an organism completely.

Output

a dictionary with information about the deleted organism

Options:

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

delete_track command

Usage:

arrow remote delete_track [OPTIONS] ORGANISM_ID TRACK_LABEL

Help

Remove a track from an organism

Output

a dictionary with information about the deleted track

Options:

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

update_organism command

Usage:

arrow remote update_organism [OPTIONS] ORGANISM_ID ORGANISM_DATA

Help

Update an organism using the remote organism API.

Output

a dictionary with information about the updated organism

Options:

--blatdb FILENAME      Path to 2bit index of the genome for Blat (Blat 2bit
                       data can also be in organism_data in directory
                       'searchDatabaseData')

--common_name TEXT     Organism common name
--genus TEXT           Genus
--species TEXT         Species
--public               User's email
--metadata TEXT        JSON formatted arbitrary metadata
--no_reload_sequences  Set this if you don't want Apollo to reload genome
                       sequences (no change in genome sequence)

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

update_track command

Usage:

arrow remote update_track [OPTIONS] ORGANISM_ID TRACK_CONFIG

Help

Update the configuration of a track that has already been added to the organism. Will not update data for the track.

Output

a dictionary with information about all tracks on the organism

Options:

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