``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:
  
.. code-block:: console

  set paths to the programs that simpleaf will use
  
  Usage: simpleaf set-paths [OPTIONS]
  
  Options:
    -p, --piscem <PISCEM>          path to piscem to use
    -a, --alevin-fry <ALEVIN_FRY>  path to alein-fry to use
    -m, --macs <MACS>              path to macs3 to use
    -h, --help                     Print help information
    -V, --version                  Print version information