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Set global options

Source: R/opts.R
set_global_opts.Rd

Convenience function for setting global options such as program paths.

Usage

set_global_opts(...)

Details

The following options can be set:

  • Required program paths (samtools, minimap2, seqtool, vsearch)

  • tmp_dir: Path to a custom temporary directory for short-lived data and not overly large data. On Linux, the default is to place these files in a subdirectory of $XDG_RUNTIME_DIR (usually /run/user/<userid>, tmpfs).

Under the hood, this simply does options(DadaNanoBC.opt = 'value', ...).

The same options can be set as environment variables: DadaNanoBC_opt=value (in R: Sys.setenv(DadaNanoBC_opt = 'value'). set_global_opt always has priority over environment variables.

Examples

set_global_opts(samtools = '/path/to/samtools', tmp_dir = '/tmp/nanopore-barcoding')