beast: Submit a BEAST or BEAST2 analysis

In fmichonneau/cipresr: An Interface to the 'CIPRES REST API' (CRA)

Description

For more information see:

• For BEAST1http://www.phylo.org/rest/beast2_xsede.html and the BEAST2 website http://beast2.org

• For BEAST2http://www.phylo.org/index.php/rest/beast_tg.html and the BEAST website http://beast.bio.ed.ac.uk

Usage

cipres_submit_beast1(input_file, beast_version = c("1.8.2", "1.8.1", "1.8.0"),
  use_beagle = TRUE, max_runtime = 10, codon_partitioning = FALSE,
  use_seed = NULL, job_name = NULL, get_email = TRUE, note = NULL, ...)

cipres_submit_beast2(input_file, beast_version = c("2.3.0", "2.1.3"),
  max_runtime = 10, use_beagle = TRUE, use_seed = NULL,
  overwrite_logs = TRUE, job_name = NULL, get_email = TRUE, note = NULL,
  ...)

Arguments

input_file	An XML input file generated by BEAUTI2
beast_version	Which version of BEAST2 should be used?
use_beagle	Should the BEAGLE library be used?
max_runtime	How long should the job run for? (in hours)
codon_partitioning	Do the partitions follow the codon positions?
use_seed	If NULL (default), a random seed will be generated by BEAST, otherwise specify your own seed.
job_name	An optional name to identify the job.
get_email	Should an email be sent when the job completed?
note	An optional character string to record notes about the job.
...	arguments to customize the API call. These arguments are passed to the appropriate httr function (GET, POST, DELETE)
overwrite_logs	Should existing log files on the server be overwritten?

Details

Specifying the number of partitions and patterns in the alignments are not required by BEAST, but are used by CIPRES to optimize the computing parameters for improved run times.

fmichonneau/cipresr documentation built on May 16, 2019, 1:44 p.m.