Usage reference

refgenie --help

version: 0.9.3
usage: refgenie [-h] [--version] [--silent] [--verbosity V] [--logdev]
                {init,list,listr,pull,build,seek,add,remove,getseq,tag,id,subscribe,unsubscribe}
                ...

refgenie - reference genome asset manager

positional arguments:
  {init,list,listr,pull,build,seek,add,remove,getseq,tag,id,subscribe,unsubscribe}
    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.
    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.

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 [-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.
  -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] [-g [GENOME [GENOME ...]]]

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.
  -g [GENOME [GENOME ...]], --genome [GENOME [GENOME ...]]
                        Reference assembly ID, e.g. mm10.

refgenie listr --help

usage: refgenie listr [-h] [-c C] [-g [GENOME [GENOME ...]]]

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.
  -g [GENOME [GENOME ...]], --genome [GENOME [GENOME ...]]
                        Reference assembly ID, e.g. mm10.

refgenie pull --help

usage: refgenie pull [-h] [-c C] [-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.
  -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] [-R] [-C CONFIG_FILE] [-N]
                      [--tag-description TAG_DESCRIPTION]
                      [--genome-description GENOME_DESCRIPTION] [-d]
                      [--assets ASSETS [ASSETS ...]]
                      [--files FILES [FILES ...]]
                      [--params PARAMS [PARAMS ...]]
                      [-v VOLUMES [VOLUMES ...]] [-o OUTFOLDER] [-q]
                      [-r RECIPE] [-g G]
                      asset-registry-paths [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.
  -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.
  --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.
  -o OUTFOLDER, --outfolder OUTFOLDER
                        Override the default path to genomes folder, which is
                        the genome_folder attribute in the genome
                        configuration file.
  -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] [-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.
  -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 add --help

usage: refgenie add [-h] [-c C] [-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.
  -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] [-g G] [-f]
                       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.
  -g G, --genome G      Reference assembly ID, e.g. mm10.
  -f, --force           Do not prompt before action, approve upfront.

refgenie getseq --help

usage: refgenie getseq [-h] [-c C] -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.
  -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] [-g G] (-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.
  -g G, --genome G      Reference assembly ID, e.g. mm10.
  -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] [-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.
  -g G, --genome G      Reference assembly ID, e.g. mm10.

refgenie subscribe --help

usage: refgenie subscribe [-h] [-c C] [-r] -s GENOME_SERVER
                          [GENOME_SERVER ...]

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.
  -r, --reset           Overwrite the current list of server URLs.
  -s GENOME_SERVER [GENOME_SERVER ...], --genome-server GENOME_SERVER [GENOME_SERVER ...]
                        One or more URLs to add to the genome_servers
                        attribute in config file.

refgenie unsubscribe --help

usage: refgenie unsubscribe [-h] [-c C] -s GENOME_SERVER [GENOME_SERVER ...]

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.
  -s GENOME_SERVER [GENOME_SERVER ...], --genome-server GENOME_SERVER [GENOME_SERVER ...]
                        One or more URLs to remove from the genome_servers
                        attribute in config file.