Use refgenie in your pipeline

The code snippets below can be used in your pipeline to assert the existence of the refgenie-managed files in 3 different languages: Bash, Python and R.

Refgenie checks if the asset is available locally and tries pull it from the server if it’s not.

The only step that needs to precede the execution of these functions is initializing refgenie’s database configuration:

refgenie init

By default this creates a local SQLite database. To use a specific configuration file, set the REFGENIE_DB_CONFIG_PATH environment variable to its path:

export REFGENIE_DB_CONFIG_PATH=/path/to/refgenie_db_config.yaml

Bash

Requirements:

• Python package refgenie

#!/bin/bash

assert_refgenie_asset_exists(){

    RED='\033[0;31m'
    GREEN='\033[0;32m'
    YELLOW='\033[0;33m'
    NC='\033[0m'

    if [ -z "$1" ]; then
        echo -e "\n${RED}Asset registry path not provided!${NC}\n"
        exit 1
    fi

    # check if refgenie env var is defined
    if [ -z "$REFGENIE_DB_CONFIG_PATH" ]
    then
        echo -e "${RED}refgenie env var not defined."
        echo -e "Run 'export REFGENIE_DB_CONFIG_PATH=<path to refgenie db config>' to set the env var.${NC}"
        exit 1
    else
        echo -e "${GREEN}refgenie env var defined: $REFGENIE_DB_CONFIG_PATH${NC}"
    fi

    # check if asset is available locally
    if file_path=`refgenie seek $1`; then
        echo -e "${GREEN}Found ($1) asset: $file_path${NC}"
    else
        # pull if not available locally
        echo -e "${YELLOW}Asset ($1) not found, pulling...${NC}"
        refgenie pull $1
        if file_path=`refgenie seek $1`; then
            echo -e "${GREEN}Asset ($1) pulled successfully: $file_path${NC}"
        else
            echo -e "${RED}Asset ($1) pull failed${NC}"
            exit 1
        fi
    fi
}


# Run like this: assert_refgenie_asset_exists hg38/fasta

Python

Requirements:

• Python package refgenie

from refgenie import Refgenie

def assert_refgenie_asset_exists(
    genome, asset_group, asset=None, seek_key=None, refgenie_config=None
):
    # instantiate Refgenie object (defaults to the local database if config is None)
    rg = Refgenie(database_config_path=refgenie_config)

    # get the asset (tag) of interest, provided vs. default
    asset = asset if asset is not None else rg.asset.get_default(asset_group, genome_name=genome)

    # check whether the asset group is missing locally
    if not rg.asset.group_exists(asset_group, genome_name=genome):
        # pull asset if missing
        print(f"{genome}/{asset_group} not found, pulling...")
        try:
            rg.pull(asset_group_name=asset_group, alias_name=genome, asset_name=asset)
        except Exception as e:
            print("Pull failed")
            raise

    # get the local path to the asset of interest
    return rg.asset.seek(
        genome_name=genome,
        asset_group_name=asset_group,
        asset_name=asset,
        seek_key_name=seek_key,
    )


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

R

Requirements:

• Python package refgenie
• R package reticulate

library('reticulate')

assertRefgenieAssetExists <-
  function(genome,
           assetGroup,
           asset = NULL,
           seek_key = NULL,
           refgenieConfig = NULL) {

    # import Python module
    refgenie = reticulate::import("refgenie", convert = FALSE)

    # determine refgenie db config path, provided vs. read from env
    refgenieConfig = ifelse(is.null(refgenieConfig),
                            Sys.getenv("REFGENIE_DB_CONFIG_PATH"),
                            refgenieConfig)

    # instantiate Python Refgenie object
    rgc = refgenie$Refgenie(database_config_path = refgenieConfig)

    # get the asset (tag) of interest, provided vs. default
    asset = ifelse(is.null(asset),
                   py_to_r(rgc$asset$get_default(assetGroup, genome_name = genome)),
                   asset)

    # string together the final asset registry path, for logging
    assetRegistryPath = paste0(genome, "/" , assetGroup, ":",  asset)

    # check whether the asset group is missing locally
    if (!py_to_r(rgc$asset$group_exists(assetGroup, genome_name = genome))) {
      # pull asset if missing
      message(paste0(assetRegistryPath, " not found, pulling..."))
      pullResult = py_to_r(rgc$pull(
        asset_group_name = assetGroup,
        alias_name = genome,
        asset_name = asset
      ))
    }

    # get the local path to the asset of interest
    seekResult = rgc$asset$seek(
      genome_name = genome,
      asset_group_name = assetGroup,
      asset_name = asset,
      seek_key_name = seek_key
    )
  }


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