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https://github.com/richelbilderbeek/peregrine

R package to work on the RuG Peregrine cluster
https://github.com/richelbilderbeek/peregrine

cluster computer-cluster groningen peregrine university

Last synced: about 2 months ago
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R package to work on the RuG Peregrine cluster

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README

        

# `peregrine`

Branch |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/richelbilderbeek/peregrine/actions) |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)
---------|-----------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------
`master` |![R-CMD-check](https://github.com/richelbilderbeek/peregrine/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/richelbilderbeek/peregrine/coverage.svg?branch=master)](https://codecov.io/github/richelbilderbeek/peregrine/branch/master)
`develop`|![R-CMD-check](https://github.com/richelbilderbeek/peregrine/workflows/R-CMD-check/badge.svg?branch=develop)|[![codecov.io](https://codecov.io/github/richelbilderbeek/peregrine/coverage.svg?branch=develop)](https://codecov.io/github/richelbilderbeek/peregrine/branch/develop)

![Peregrine falcon, by Christopher Watson](pics/peregrine_falcon.jpg)

`peregrine` is:

* [A collection of notes](doc/README.md) on the Groningen Peregrine computer cluster
* [A collection of scripts](scripts/README.md) 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)](http://richelbilderbeek.nl/peregrine_call_r_script.ogv) [YouTube](https://youtu.be/Xf8IZwR9T8U)
* How to install the pirouette R package on Peregrine [download (.ogv)](http://richelbilderbeek.nl/peregrine_install_pirouette.ogv) [YouTube](https://youtu.be/ZgAe_e7Vwy0)
* How to run a pirouette example on Peregrine [download (.ogv)](http://richelbilderbeek.nl/peregrine_run_pirouette_example.ogv) [YouTube](https://youtu.be/wnz6l_2e_-c)

## Presentations

* Running (independent) jobs on the Peregrine computer cluster [PDF](independent_jobs.pdf) [ODP](independent_jobs.odp)
* Running jobs with dependencies on the Peregrine computer cluster [PDF](job_dependencies.pdf) [ODP](job_dependencies.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!

```r
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