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bsub

Send R code/R scripts/shell commands to LSF cluster without leaving R

https://github.com/jokergoo/bsub

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Send R code/R scripts/shell commands to LSF cluster without leaving R

Basic Info
Statistics
  • Stars: 26
  • Watchers: 2
  • Forks: 5
  • Open Issues: 7
  • Releases: 0
Created over 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

Submitter and Monitor of the LSF Cluster

R-CMD-check CRAN

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 = bsubchunk(...) job2 = bsubchunk(...) 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:

View job log:

r job_log(job_id)

Interactive job monitor

r monitor()

The job summary table:

monitor

Job log:

job_log

Job dependency diagram:

dependency_graph

License

MIT @ Zuguang Gu

Owner

  • Name: Zuguang Gu
  • Login: jokergoo
  • Kind: user
  • Location: Heidelberg, Germany
  • Company: German Cancer Research Center

A bioinformagician

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 189
  • Total Committers: 3
  • Avg Commits per committer: 63.0
  • Development Distribution Score (DDS): 0.037
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zuguang Gu j****o@g****m 182
cola-recount2 z****u@d****e 6
Zuguang Gu g****z@B****x 1
Committer Domains (Top 20 + Academic)
b069-mb04.fritz.box: 1 dfkz.de: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 39
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 6
  • Total pull request authors: 0
  • Average comments per issue: 0.69
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 0
  • Average time to close issues: about 9 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jokergoo (34)
  • HJ234 (1)
  • m4gold (1)
  • Christian-Heyer (1)
  • simplifyEnrichment (1)
  • chenu (1)
Pull Request Authors
Top Labels
Issue Labels
shiny (7)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 335 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: bsub

Submitter and Monitor of the 'LSF Cluster'

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 335 Last month
Rankings
Stargazers count: 14.6%
Forks count: 14.9%
Dependent packages count: 29.8%
Average: 31.0%
Dependent repos count: 35.5%
Downloads: 60.4%
Maintainers (1)
z.gu@dkfz.de
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • GetoptLong >= 0.1.8 imports
  • GlobalOptions >= 0.1.1 imports
  • clisymbols * imports
  • codetools * imports
  • crayon * imports
  • digest * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • utils * imports
  • DT >= 0.13 suggests
  • Rgraphviz * suggests
  • ggplot2 * suggests
  • graph * suggests
  • igraph * suggests
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • shiny >= 1.0.0 suggests
  • shinyjqui * suggests
  • ssh * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite