set-paths command

The set-paths command is used to set the paths to the relevant executables and store them in a configuration file in the ALEVIN_FRY_HOME directory. If you don’t provide an explicit path for a program, simpleaf will look in your PATH for a compatible version. Once paths are set with this command, they are cached in a file in the ALEVIN_FRY_HOME directory, and used to execute other commands in simpleaf. If you wish to update the paths, you can run this command again, and it will overwrite this cache. This command takes the following optional arguments:

set paths to the programs that simpleaf will use

Usage: simpleaf set-paths [OPTIONS]

Options:
  -s, --salmon <SALMON>          path to salmon to use
  -p, --piscem <PISCEM>          path to piscem to use
  -a, --alevin-fry <ALEVIN_FRY>  path to alein-fry to use
  -h, --help                     Print help information
  -V, --version                  Print version information