cstacks_setup: batch setup cstacks For each combination of N and set of...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

batch setup cstacks For each combination of N and set of ustacks, this function creates a bash job file to run cstacks. The output of this function is a character string vector with paths to bash job files, which can be piped to the function 'rsbatch' to submit the jobs.

Description

batch setup cstacks

For each combination of N and set of ustacks, this function creates a bash job file to run cstacks. The output of this function is a character string vector with paths to bash job files, which can be piped to the function 'rsbatch' to submit the jobs.

Usage

cstacks_setup(save.in, n = 1, p = 16, cstacks.path = NULL)

Arguments

save.in	Character string with directory where output directories and files should be saved. This should be the same as the value used for the 'save.in' argument of ustacks_setup.
n	Number or numerical vector with number of mismatches allowed between sample loci when build the catalog. Default 1.
p	Number of threads to use for job parallization. Default 16.
cstacks.path	Character string with path to the cstacks executable. Default NULL, in which case the path is derived from the default setting, which can be set with config_miscwrappers('<path/to/cstacks>').

Value

Character string vector with the paths to bash job files.

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.