bsub v1.0.0

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Submitter and Monitor of the 'LSF Cluster'

It submits R code/R scripts/shell commands to 'LSF cluster' (<https://en.wikipedia.org/wiki/Platform_LSF>, the 'bsub' system) without leaving R. There is also an interactive 'shiny' app for monitoring the job status.

Functions in bsub

Name Description
bsub_opt Parameters for bsub
monitor A browser-based interactive job monitor
run_cmd Run command on submission node
job_status_by_name Job status by name
retrieve_var Retrieve saved variable
wait_jobs Wait until all jobs are finished
bsub_cmd Submit shell commands
check_dump_files Check whether there are dump files
print.bjobs Summary of jobs
random_job Submit a random job
clear_temp_dir Clear temporary dir
get_dependency Get the dependency of current jobs
job_log Log for the running/finished/failed job
bsub_script Submit R script
plot_dependency Plot the job dependency tree
job_status_by_id Job status by id
print.bconf Print the configurations
is_job_finished Test whether the jobs are finished
ssh_disconnect Disconnect ssh connection
ssh_connect Connect to submisstion via ssh
brecent Recent jobs from all status
bkill Kill jobs
bjobs_exit Failed jobs
bjobs_done Finished jobs
bconf Print current configuation
bjobs Summary of jobs
bsub_chunk Submit R code
bjobs_running Running jobs
bjobs_pending Pending jobs
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Details

Type Package
Date 2020-07-25
biocViews Software, Infrastructure
URL https://github.com/jokergoo/bsub
License MIT + file LICENSE
NeedsCompilation no
SystemRequirements Platform LSF, bsub
Packaged 2020-07-25 11:43:10 UTC; jokergoo
Repository CRAN
Date/Publication 2020-07-30 11:00:06 UTC

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