Usage reference

refgenie --help

version: 0.7.0
usage: refgenie [-h] [--version] [--silent] [--verbosity V] [--logdev]
                {init,list,listr,pull,build,seek,add,remove,getseq,tag} ...

refgenie - builds and manages reference genome assemblies

positional arguments:
  {init,list,listr,pull,build,seek,add,remove,getseq,tag}
    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                 Assign a selected tag to an asset.

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 GENOME_CONFIG [-s GENOME_SERVER]

Initialize a genome configuration.

optional arguments:
  -h, --help            show this help message and exit
  -c GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -s GENOME_SERVER, --genome-server GENOME_SERVER
                        URL to use for the genome_server attribute in config
                        file. Default: http://refgenomes.databio.org

refgenie list --help

usage: refgenie list [-h] [-c GENOME_CONFIG] [-g GENOME]

List available local assets.

optional arguments:
  -h, --help            show this help message and exit
  -c GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10

refgenie listr --help

usage: refgenie listr [-h] [-c GENOME_CONFIG] [-g GENOME]

List available remote assets.

optional arguments:
  -h, --help            show this help message and exit
  -c GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10

refgenie pull --help

usage: refgenie pull [-h] [-c GENOME_CONFIG] [-g GENOME] [-u]
                     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 GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10
  -u, --no-untar        Do not extract tarballs.

refgenie build --help

usage: refgenie build [-h] [-c GENOME_CONFIG] [-R] [-C CONFIG_FILE] [-N] [-d]
                      [-t TAGS [TAGS ...]] [-v VOLUMES [VOLUMES ...]]
                      [-o OUTFOLDER] [-r] [-g GENOME]
                      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 GENOME_CONFIG, --genome-config GENOME_CONFIG
                        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
  -d, --docker          Run all commands in the refgenie docker container.
  -t TAGS [TAGS ...], --tags TAGS [TAGS ...]
                        Override the default tags of the parent assets (e.g.
                        asset:tag).
  -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.
  -r, --requirements    Show the build requirements for the specified asset.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10

refgenie seek --help

usage: refgenie seek [-h] [-c GENOME_CONFIG] [-g GENOME]
                     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 GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10

refgenie add --help

usage: refgenie add [-h] [-c GENOME_CONFIG] [-g GENOME] -p PATH
                    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 GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10
  -p PATH, --path PATH  Relative local path to asset

refgenie remove --help

version: 0.5.0
usage: refgenie remove [-h] [-c GENOME_CONFIG] -g GENOME
                       [-a ASSET [ASSET ...]]

Remove a local asset.

optional arguments:
  -h, --help            show this help message and exit
  -c GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10
  -a ASSET [ASSET ...], --asset ASSET [ASSET ...]
                        Name of one or more assets (keys in genome config
                        file)

refgenie getseq --help

usage: refgenie getseq [-h] [-c GENOME_CONFIG] -g GENOME -l LOCUS

Get sequences from a genome.

optional arguments:
  -h, --help            show this help message and exit
  -c GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10
  -l LOCUS, --locus LOCUS
                        Coordinates to retrieve sequence for; such has
                        'chr1:50000-50200'.

refgenie tag --help

usage: refgenie tag [-h] [-c GENOME_CONFIG] [-g GENOME] -t TAG
                    asset-registry-paths [asset-registry-paths ...]

Assign a selected tag to 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 GENOME_CONFIG, --genome-config GENOME_CONFIG
                        Path to local genome configuration file. Optional if
                        REFGENIE environment variable is set.
  -g GENOME, --genome GENOME
                        Reference assembly ID, e.g. mm10
  -t TAG, --tag TAG     Tag to assign to an asset