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.