Use refgenie in your pipeline

These snippets make sure a refgenie asset is present before a pipeline uses it, in Bash, Python, and R. Each one looks for the asset locally, pulls it from your server if it is missing, and returns its path.

Run refgenie init once first. By default refgenie uses a local SQLite database; to use another database, set REFGENIE_DB_CONFIG_PATH to its configuration file.

Bash

Needs the refgenie Python package.

#!/bin/bash

assert_refgenie_asset_exists(){
    if [ -z "$1" ]; then
        echo "Asset registry path not provided!" >&2
        exit 1
    fi

    if file_path=$(refgenie seek "$1"); then
        echo "Found ($1) asset: $file_path" >&2
    else
        echo "Asset ($1) not found, pulling..." >&2
        refgenie pull "$1"
        if ! file_path=$(refgenie seek "$1"); then
            echo "Asset ($1) pull failed" >&2
            exit 1
        fi
    fi
    echo "$file_path"
}

# Run like this: assert_refgenie_asset_exists hg38/fasta

Python

Needs the refgenie Python package.

from refgenie import GenomeAlias, Refgenie
from refgenie.exceptions import MissingAliasError


def assert_refgenie_asset_exists(
    genome, asset_group, asset=None, seek_key=None, refgenie_config=None
):
    # uses the default database when refgenie_config is None
    rg = Refgenie(database_config_path=refgenie_config)
    alias = GenomeAlias(genome)

    try:
        digest = rg.alias.resolve(alias)
        have_group = rg.asset.group.exists(asset_group, genome_digest=digest)
    except MissingAliasError:
        have_group = False

    if not have_group:
        print(f"{genome}/{asset_group} not found, pulling...")
        rg.transfer.pull(asset_group_name=asset_group, genome=alias, asset_name=asset)
        digest = rg.alias.resolve(alias)

    # the group's default asset and seek key unless given
    return rg.asset.seek(digest, asset_group, asset_name=asset, seek_key_name=seek_key)


# Run like this: assert_refgenie_asset_exists(genome="hg38", asset_group="fasta")

R

Needs the refgenie Python package and the R package reticulate.

library(reticulate)

assertRefgenieAssetExists <- function(genome, assetGroup, asset = NULL, seekKey = NULL) {
  refgenie <- reticulate::import("refgenie")

  rg <- refgenie$Refgenie()
  alias <- refgenie$GenomeAlias(genome)

  haveGroup <- tryCatch({
    digest <- rg$alias$resolve(alias)
    rg$asset$group$exists(assetGroup, genome_digest = digest)
  }, error = function(e) FALSE)

  if (!haveGroup) {
    message(paste0(genome, "/", assetGroup, " not found, pulling..."))
    rg$transfer$pull(asset_group_name = assetGroup, genome = alias, asset_name = asset)
  }

  digest <- rg$alias$resolve(alias)
  rg$asset$seek(digest, assetGroup, asset_name = asset, seek_key_name = seekKey)
}

# Run like this: assertRefgenieAssetExists(genome = "hg38", assetGroup = "fasta")