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

cipresr :deciduous_tree:

R client to the CIPRES API.

CIPRES (Cyber Infrastructure for Phylogenetic Research) is a popular service that gives researchers easy access to NSF's large computional resources (XSEDE) for phylogenetic inference.

This package allows researchers to submit jobs to CIPRES directly from R. By enabling access to large computational resources within the analytical workflow, cipresr intends to facilitate reproducibility, as researchers don't need to navigate through several web pages and click checkboxes to submit their analysis.

This package is in active development and can currently be used to submit RAxML, BEAST (v1.8.x), and BEAST2 analyses. A few other tools will soon be added.

Installation

The package is not available on CRAN and it needs to be installed from GitHub:

devtools::install_github("richfitz/storr")
devtools::install_github("fmichonneau/cipresr")

After the installation, you will need to create an account to use the CIPRES REST services (this is different from the account you may already have to access the CIPRES web interface).

Then you can type:

library(cipresr)
cipres_setup()

This function will take you through the required steps to set up cipresr. We use Rich FitzJohn's storr package to store your login credentials on your hard drive. Thus, you only need to enter your login information once.

Once setup, you can submit your jobs, and get the results once the analysis is done, using cipresr:

cipres_submit_beast2(input_file = "my_analysis.xml", n_patterns = 1000, n_partitions = 5)
cipres_download("NGBW-JOB-BEAST2_XSEDE-66666666666666666666", "~/my_analysis_results/")

Don't hesitate to open an issue if you'd like to have access to a tool other than BEAST and RAxML.