`peregrine`

Branch
`master`
`develop`

peregrine is:

A collection of notes on the Groningen Peregrine computer cluster
A collection of scripts for the Groningen Peregrine computer cluster
An R package for some Peregrine functions
Some presentations on the Groningen Peregrine computer cluster (see below)

Videos

How to run an R script on Peregrine download (.ogv) YouTube
How to install the pirouette R package on Peregrine download (.ogv) YouTube
How to run a pirouette example on Peregrine download (.ogv) YouTube

Presentations

Running (independent) jobs on the Peregrine computer cluster PDF ODP
Running jobs with dependencies on the Peregrine computer cluster PDF ODP

Example

The most important function is is_pff: 'Is Peregrine-friendly Filename/Folder'. If this function returns FALSE, one better not uses that path on the Peregrine cluster!

library(peregrine)
library(testthat)

expect_true(is_pff(get_pff_tempdir()))
expect_true(is_pff(get_pff_tempfile()))
expect_false(is_pff("/local/tmp/peregrine_unfriendly"))
expect_false(is_pff("/tmp/peregrine_unfriendly"))

One can use to_pff to convert a filename or folder to its Peregrine-friendly equivalent.

Measurements

Using scripts/test_is_pff.R.

Can create file?

filename	`can_create_file`
`/local/tmp.txt`	TRUE
`/local/tmp/tmp.txt`	TRUE
`/tmp.txt`	FALSE
`/tmp/tmp.txt`	TRUE
`/data/tmp.txt`	FALSE
`/data/p230198/tmp.txt`	TRUE
`/home/p230198/tmp.txt`	TRUE
`/home/tmp.txt`	FALSE

Can start BEAST2?

prefix	`can_start_beast`
`/local`	TRUE
`/local/tmp`	TRUE
`/tmp`	FALSE
`/`	FALSE
`/data`	FALSE
`/data/p230198`	FALSE
`/home`	FALSE
`/home/p230198`	FALSE

Can use BEAST2?

folder_name	`can_use_beast`
`/tmp	FALSE
`/local/tmp	TRUE
`/data/p230198	FALSE
`/home/p230198	TRUE

Can use working dir?

folder_name	`can_use_working_dir`
`/tmp`	FALSE
`/local/tmp`	FALSE
`/data/p230198`	FALSE
`/home/p230198`	TRUE

richelbilderbeek/peregrine

peregrine