| Branch |  |
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|---|---|---|
master |
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develop |
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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)
- 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
- Running (independent) jobs on the Peregrine computer cluster PDF ODP
- Running jobs with dependencies on the Peregrine computer cluster PDF ODP
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.
Using scripts/test_is_pff.R.
| 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 |
| prefix | can_start_beast |
|---|---|
/local |
TRUE |
/local/tmp |
TRUE |
/tmp |
FALSE |
/ |
FALSE |
/data |
FALSE |
/data/p230198 |
FALSE |
/home |
FALSE |
/home/p230198 |
FALSE |
| folder_name | can_use_beast |
|---|---|
| `/tmp | FALSE |
| `/local/tmp | TRUE |
| `/data/p230198 | FALSE |
| `/home/p230198 | TRUE |
| folder_name | can_use_working_dir |
|---|---|
/tmp |
FALSE |
/local/tmp |
FALSE |
/data/p230198 |
FALSE |
/home/p230198 |
TRUE |