gdc_client: return gdc-client executable path

In GenomicDataCommons: NIH / NCI Genomic Data Commons Access

Description

This function is a convenience function to find and return the path to the GDC Data Transfer Tool executable assumed to be named 'gdc-client'. The assumption is that the appropriate version of the GDC Data Transfer Tool is a separate download available from https://gdc.cancer.gov/access-data/gdc-data-transfer-tool and as a backup from https://github.com/NCI-GDC/gdc-client.

Usage

gdc_client()

Details

The path is checked in the following order:

1. an R option("gdc_client")

2. an environment variable GDC_CLIENT

3. from the search PATH

4. in the current working directory

Value

character(1) the path to the gdc-client executable.

Examples

# this cannot run without first
# downloading the GDC Data Transfer Tool
gdc_client = try(gdc_client(),silent=TRUE)

GenomicDataCommons documentation built on Nov. 8, 2020, 11:08 p.m.