https://github.com/jokergoo/bsub

Send R code/R scripts/shell commands to LSF cluster without leaving R
https://github.com/jokergoo/bsub

Last synced: 24 days ago
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Send R code/R scripts/shell commands to LSF cluster without leaving R

• Host: GitHub
• URL: https://github.com/jokergoo/bsub
• Owner: jokergoo
• License: other
• Created: 2019-11-07T22:40:28.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2024-03-30T07:08:15.000Z (7 months ago)
• Last Synced: 2024-05-09T07:44:53.714Z (6 months ago)
• Language: R
• Homepage: https://jokergoo.github.io/bsub
• Size: 1.45 MB
• Stars: 23
• Watchers: 3
• Forks: 4
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Submitter and Monitor of the LSF Cluster

[![R-CMD-check](https://github.com/jokergoo/bsub/workflows/R-CMD-check/badge.svg)](https://github.com/jokergoo/bsub/actions)

[![CRAN](https://www.r-pkg.org/badges/version/bsub)](https://cran.r-project.org/web/packages/bsub/index.html)

It sends R code/R scripts/shell commands to LSF cluster without leaving R.

### Install

Directly from CRAN:

```r

install.packages("bsub")

```

Or from GitHub:

```r

if (!requireNamespace("devtools", quietly = TRUE))

    install.packages("devtools")

devtools::install_github("jokergoo/bsub")

```

### Documentation

The online documentation is available at https://jokergoo.github.io/bsub/.

### Submit jobs

Directly submit R chunk:

```r

library(bsub)

# R code

bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4, 

{

    fit = NMF::nmf(...)

    # you better save `fit` into a permanent file

    saveRDS(fit, file = "/path/of/fit.rds")

})

```

Submit an R script:

```r

# R script

bsub_script(name = "example",

    script = "/path/of/foo.R", ...)

```

Submit shell commands:

```r

# shell commands

bsub_cmd(name = "example",

    cmd = "samtools view ...", ...)

```

Kill jobs:

```r

bkill(job_id)

```

### Job dependencies

```r

job1 = bsub_chunk(...)

job2 = bsub_chunk(...)

bsub_chunk(..., dependency = c(job1, job2))

```

### View job info

View job summaries:

```r

bjobs

brecent

bjobs_running

bjobs_pending

bjobs_done

bjobs_exit

```

An example of the job queries is as follows:

![](https://user-images.githubusercontent.com/449218/71292253-2577ad00-2374-11ea-9402-855e7f01652c.png)

View job log: 

```r

job_log(job_id)

```

### Interactive job monitor

```r

monitor()

```

The job summary table:



Job log:



Job dependency diagram:



### License

MIT @ Zuguang Gu