Usage reference
refgenie --help
version: 0.11.1-dev | refgenconf 0.11.2-dev
usage: refgenie [-h] [--version] [--silent] [--verbosity V] [--logdev]
{init,list,listr,pull,build,seek,seekr,add,remove,getseq,tag,id,subscribe,unsubscribe,alias,compare,upgrade,populate,populater}
...
refgenie - reference genome asset manager
positional arguments:
{init,list,listr,pull,build,seek,seekr,add,remove,getseq,tag,id,subscribe,unsubscribe,alias,compare,upgrade,populate,populater}
init Initialize a genome configuration.
list List available local assets.
listr List available remote assets.
pull Download assets.
build Build genome assets.
seek Get the path to a local asset.
seekr Get the path to a remote asset.
add Add local asset to the config file.
remove Remove a local asset.
getseq Get sequences from a genome.
tag Tag an asset.
id Return the asset digest.
subscribe Add a refgenieserver URL to the config.
unsubscribe Remove a refgenieserver URL from the config.
alias Interact with aliases.
compare Compare two genomes.
upgrade Upgrade config. This will alter the files on disk.
populate Populate registry paths with local paths.
populater Populate registry paths with remote paths.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--silent Silence logging. Overrides verbosity.
--verbosity V Set logging level (1-5 or logging module level name)
--logdev Expand content of logging message format.
https://refgenie.databio.org
refgenie init --help
usage: refgenie init [-h] -c C [--skip-read-lock] [-s GENOME_SERVER [GENOME_SERVER ...]]
[-f GENOME_FOLDER] [-a GENOME_ARCHIVE_FOLDER]
[-b GENOME_ARCHIVE_CONFIG] [-u REMOTE_URL_BASE] [-j SETTINGS_JSON]
Initialize a genome configuration.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-s GENOME_SERVER [GENOME_SERVER ...], --genome-server GENOME_SERVER [GENOME_SERVER ...]
URL(s) to use for the genome_servers attribute in
config file. Default:
http://refgenomes.databio.org.
-f GENOME_FOLDER, --genome-folder GENOME_FOLDER
Absolute path to parent folder refgenie-managed
assets.
-a GENOME_ARCHIVE_FOLDER, --genome-archive-folder GENOME_ARCHIVE_FOLDER
Absolute path to parent archive folder refgenie-
managed assets; used by refgenieserver.
-b GENOME_ARCHIVE_CONFIG, --genome-archive-config GENOME_ARCHIVE_CONFIG
Absolute path to desired archive config file; used
by refgenieserver.
-u REMOTE_URL_BASE, --remote-url-base REMOTE_URL_BASE
URL to use as an alternative, remote archive
location; used by refgenieserver.
-j SETTINGS_JSON, --settings-json SETTINGS_JSON
Absolute path to a JSON file with the key value
pairs to inialize the configuration file with.
Overwritten by itemized specifications.
refgenie list --help
usage: refgenie list [-h] [-c C] [--skip-read-lock] [-g [G ...]] [-r]
List available local assets.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if
REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g [G ...], --genome [G ...] Reference assembly ID, e.g. mm10.
-r, --recipes List available recipes.
refgenie listr --help
usage: refgenie listr [-h] [-c C] [--skip-read-lock] [-g [G ...]] [-s S [S ...]] [-p]
List available remote assets.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-g [G ...], --genome [G ...] Reference assembly ID, e.g. mm10.
-s S [S ...], --genome-server S [S ...]
One or more URLs to use. This information will not
persist in the genome config file.
-p, --append-server Whether the provided servers should be appended to
the list.
refgenie pull --help
usage: refgenie pull [-h] [-c C] [--skip-read-lock] [-g G]
[--no-overwrite | --force-overwrite] [--no-large | --pull-large]
[--size-cutoff S] [-b]
asset-registry-paths [asset-registry-paths ...]
Download assets.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
Prompt handling:
These flags configure the pull prompt responses.
--no-overwrite Do not overwrite if asset exists.
--force-overwrite Overwrite if asset exists.
--no-large Do not pull archives over 5GB.
--pull-large Pull any archive, regardless of its size.
--size-cutoff S Maximum archive file size to download with no confirmation
required (in GB, default: 10)
-b, --batch Use batch mode: pull large archives, do no overwrite
refgenie build --help
usage: refgenie build [-h] [-c C] [--skip-read-lock] [-R] [-C CONFIG_FILE] [-N]
[--tag-description TAG_DESCRIPTION]
[--genome-description GENOME_DESCRIPTION] [-d] [--map]
[--pull-parents] [--reduce] [--assets ASSETS [ASSETS ...]]
[--files FILES [FILES ...]] [--params PARAMS [PARAMS ...]]
[-v VOLUMES [VOLUMES ...]] [-q] [-r RECIPE] [-g G]
[asset-registry-paths ...]
Build genome assets.
positional arguments:
asset-registry-paths One or more registry path strings that identify
assets (e.g. hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-R, --recover Overwrite locks to recover from previous failed
run
-C CONFIG_FILE, --config CONFIG_FILE Pipeline configuration file (YAML). Relative paths
are with respect to the pipeline script.
-N, --new-start Overwrite all results to start a fresh run
--tag-description TAG_DESCRIPTION Add tag level description (e.g. built with version
0.3.2).
--genome-description GENOME_DESCRIPTION
Add genome level description (e.g. The mouse
mitochondrial genome, released in Dec 2013).
-d, --docker Run all commands in the refgenie docker container.
--map Run the map procedure: build assets and store the
metadata in separate configs.
--pull-parents Automatically pull the default parent asset if
required but not provided
--reduce Run the reduce procedure: gather the metadata
produced with `refgenie build --map`.
--assets ASSETS [ASSETS ...] Override the default genome, asset and tag of the
parents (e.g. fasta=hg38/fasta:default
gtf=mm10/gencode_gtf:default).
--files FILES [FILES ...] Provide paths to the required files (e.g.
fasta=/path/to/file.fa.gz).
--params PARAMS [PARAMS ...] Provide required parameter values (e.g.
param1=value1).
-v VOLUMES [VOLUMES ...], --volumes VOLUMES [VOLUMES ...]
If using docker, also mount these folders as
volumes.
-q, --requirements Show the build requirements for the specified
asset and exit.
-r RECIPE, --recipe RECIPE Provide a recipe to use.
-g G, --genome G Reference assembly ID, e.g. mm10.
refgenie seek --help
usage: refgenie seek [-h] [-c C] [--skip-read-lock] [-g G] [-e]
asset-registry-paths [asset-registry-paths ...]
Get the path to a local asset.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag or hg38/fasta.fai:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-e, --check-exists Whether the returned asset path should be checked for existence
on disk.
refgenie seekr --help
usage: refgenie seekr [-h] [-c C] [--skip-read-lock] [-g G] [-s S [S ...]] [-p]
[--remote-class RC]
asset-registry-paths [asset-registry-paths ...]
Get the path to a remote asset.
positional arguments:
asset-registry-paths One or more registry path strings that identify
assets (e.g. hg38/fasta or hg38/fasta:tag or
hg38/fasta.fai:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-s S [S ...], --genome-server S [S ...]
One or more URLs to use. This information will not
persist in the genome config file.
-p, --append-server Whether the provided servers should be appended to
the list.
--remote-class RC Remote data provider class, e.g. 'http' or 's3'
refgenie populate --help
usage: refgenie populate [-h] [-c C] [--skip-read-lock] [-f F]
Populate registry paths with local paths.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-f F, --file F File with registry paths to populate
refgenie populater --help
usage: refgenie populater [-h] [-c C] [--skip-read-lock] [-s S [S ...]] [-p]
[--remote-class RC] [-f F]
Populate registry paths with remote paths.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-s S [S ...], --genome-server S [S ...]
One or more URLs to use. This information will not
persist in the genome config file.
-p, --append-server Whether the provided servers should be appended to
the list.
--remote-class RC Remote data provider class, e.g. 'http' or 's3'
-f F, --file F File with registry paths to populate
refgenie add --help
usage: refgenie add [-h] [-c C] [--skip-read-lock] [-g G] [-f] -p P [-s S]
asset-registry-paths [asset-registry-paths ...]
Add local asset to the config file.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-f, --force Do not prompt before action, approve upfront.
-p P, --path P Relative local path to asset.
-s S, --seek-keys S String representation of a JSON object with seek_keys, e.g.
'{"seek_key1": "file.txt"}'
refgenie remove --help
usage: refgenie remove [-h] [-c C] [--skip-read-lock] [-g G] [-f] [-a]
asset-registry-paths [asset-registry-paths ...]
Remove a local asset.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-f, --force Do not prompt before action, approve upfront.
-a, --aliases Remove the genome alias if last asset for that genome is
removed.
refgenie getseq --help
usage: refgenie getseq [-h] [-c C] [--skip-read-lock] -g G -l LOCUS
Get sequences from a genome.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-l LOCUS, --locus LOCUS Coordinates of desired sequence; e.g. 'chr1:50000-50200'.
refgenie tag --help
usage: refgenie tag [-h] [-c C] [--skip-read-lock] [-g G] [-f] (-t TAG | -d)
asset-registry-paths [asset-registry-paths ...]
Tag an asset.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
-f, --force Do not prompt before action, approve upfront.
-t TAG, --tag TAG Tag to assign to an asset.
-d, --default Set the selected asset tag as the default one.
refgenie id --help
usage: refgenie id [-h] [-c C] [--skip-read-lock] [-g G]
asset-registry-paths [asset-registry-paths ...]
Return the asset digest.
positional arguments:
asset-registry-paths One or more registry path strings that identify assets (e.g.
hg38/fasta or hg38/fasta:tag).
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-g G, --genome G Reference assembly ID, e.g. mm10.
refgenie subscribe --help
usage: refgenie subscribe [-h] [-c C] [--skip-read-lock] [-r] -s S [S ...]
Add a refgenieserver URL to the config.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-r, --reset Overwrite the current list of server URLs.
-s S [S ...], --genome-server S [S ...]
One or more URLs to add to the genome_servers
attribute in config file.
refgenie unsubscribe --help
usage: refgenie unsubscribe [-h] [-c C] [--skip-read-lock] -s S [S ...]
Remove a refgenieserver URL from the config.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional
if REFGENIE environment variable is set.
--skip-read-lock Whether the config file should not be locked for
reading
-s S [S ...], --genome-server S [S ...]
One or more URLs to remove from the genome_servers
attribute in config file.
refgenie alias --help
usage: refgenie alias [-h] {remove,set,get} ...
Interact with aliases.
positional arguments:
{remove,set,get}
remove Remove aliases.
set Set aliases.
get Get aliases.
optional arguments:
-h, --help show this help message and exit
refgenie upgrade --help
usage: refgenie upgrade [-h] [-c C] [--skip-read-lock] -v V [-f]
Upgrade config. This will alter the files on disk.
optional arguments:
-h, --help show this help message and exit
-c C, --genome-config C Path to local genome configuration file. Optional if REFGENIE
environment variable is set.
--skip-read-lock Whether the config file should not be locked for reading
-v V, --target-version V Target config version for the upgrade.
-f, --force Do not prompt before action, approve upfront.