manage_paths: organise and test external dependencies
In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description Usage Arguments Value Examples

This function checks that all the external dependencies required for secertome prediction pipelines are available and can sucessfully pass test runs.

All the external dependencies can be made accessible via $PATH environment variable; alternatively a text file the with full paths to all the external dependencies should be provided.

For the instalation instructions please see SecretSanta vignette.

1 2	manage_paths(in_path = c(TRUE, FALSE), test_tool = c("all", "signalp2", "signalp3", "signalp4", "targetp", "tmhmm", "wolfpsort"), path_file = NULL)

`in_path`	if TRUE manage_paths will attempt to run external dependencies, assuming that respective paths are attached to the $PATH variable; if FALSE you should supply path_file.
`test_tool`	if all - all the external dependencies will be checked; alternatively specify a tool name to be checked.
`path_file`	full paths to external dependencies in a 2-column space-separated text file; for multiple versions of signalp please use 'signalpV'notation, where V is a version number; first column should contain tool name; second column should contain full path to the tool's executable.

a list of length 3 with the following elements:

tests TRUE if all the exteranl dependencies are working;
in_path TRUE if the dependecies are accessible via $PATH; FALSE - if paths are provided with the path_file argument;
path_tibble a tibble with verified names and paths for external dependencies;
NA if in_path is TRUE;
if a specific tool is tested, a singualr path will be returned.

# Example1:
# here we assume that paths to all the
# external dependencies are attached to
# the $PATH variable:

manage_paths(in_path = TRUE, test_tool = 'all')

# to test just a single tool:
manage_paths(in_path = TRUE, test_tool = 'signalp2')

# Example2:
# alternatively, we are in a situation
# when changing $PATH is not possible,
# so we supply a file with listed full
# paths to the external dependencies:

manage_paths(in_path = FALSE,
test_tool = 'all',
path_file = system.file("extdata", "sample_paths", package = "SecretSanta"))