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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
- Host: GitHub
- URL: https://github.com/richelbilderbeek/peregrine
- Owner: richelbilderbeek
- Created: 2016-06-14T07:47:09.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-03-24T08:48:17.000Z (9 months ago)
- Last Synced: 2024-10-10T20:11:18.824Z (3 months ago)
- Topics: cluster, computer-cluster, groningen, peregrine, university
- Language: R
- Homepage:
- Size: 1.21 MB
- Stars: 3
- Watchers: 4
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# `peregrine`
Branch |[](https://github.com/richelbilderbeek/peregrine/actions) |[](https://www.codecov.io)
---------|-----------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------
`master` | |[](https://codecov.io/github/richelbilderbeek/peregrine/branch/master)
`develop`||[](https://codecov.io/github/richelbilderbeek/peregrine/branch/develop)
`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