Welcome to the documentation for simpleaf#
What is simpleaf?#
simpleaf is a program to simplify and customize the running and
configuration of single-cell processing with alevin-fry.
This documentation covers the main commands of simpleaf, and how the program works.
The tutorials we have made for simpleaf are available at alevin-fry tutorial website.
Important note#
The simpleaf program runs tools uses in the alevin-fry pipeline. Specifically,
to make use of the core functionality of this tool, you will need to install
piscem (and / or salmon) and
alevin-fry. Further, in order to operate properly,
simpleaf requires that you set the environment variable ALEVIN_FRY_HOME. It will use the directory
pointed to by this variable to cache useful information (e.g. the paths to selected versions of
the tools mentioned above, the mappings for custom chemistries you tell it about, and other information
like the permit lsits for certain chemistries). So, before you run simpleaf, please make sure that you
set the ALEVIN_FRY_HOME environment variable (you can also set it on the command line when you run
simpleaf, but setting it in your environment once is much simpler). In most shells, this can be done with
$ export ALEVIN_FRY_HOME=/full/path/to/dir/you/want/to/use
That’s it for initial notes. Use the menu below to learn more about the simpleaf commands.