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peregrine

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Peregrine falcon, by Christopher Watson

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

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

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