Package: submitr 0.1.0.9000

Erwin Lares

submitr: Scaffold and Submit Computational Jobs to CHTC Schedulers

Provides scaffolding tools to help researchers prepare and submit computational jobs to high-throughput computing (HTC) schedulers. Generates the files required to run containerized R analyses on 'HTCondor', including submit files and executable scripts, and wraps the system commands needed to stage files, submit jobs, monitor status, and retrieve results from a CHTC submit node. A session-level job manifest tracks metadata across the workflow so that result files can be downloaded automatically without constructing file lists by hand. Provides 'htc_start()' for session management and 'htc_config()' for connection details and SSH connection reuse guidance. Works naturally alongside 'containr' for container image management and 'toolero' for dataset splitting and project scaffolding.

Authors:Erwin Lares [aut, cre]

submitr_0.1.0.9000.tar.gz
submitr_0.1.0.9000.zip(r-4.7)submitr_0.1.0.9000.zip(r-4.6)submitr_0.1.0.9000.zip(r-4.5)
submitr_0.1.0.9000.tgz(r-4.6-any)submitr_0.1.0.9000.tgz(r-4.5-any)
submitr_0.1.0.9000.tar.gz(r-4.7-any)submitr_0.1.0.9000.tar.gz(r-4.6-any)
submitr_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
submitr/json (API)

# Install 'submitr' in R:
install.packages('submitr', repos = c('https://erwinlares.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/erwinlares/submitr/issues

Pkgdown/docs site:https://erwinlares.github.io

On CRAN:

Conda:

4.97 score 1 stars 31 scripts 528 downloads 8 exports 25 dependencies

Last updated from:e47270da37. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK164
source / vignettesOK168
linux-release-x86_64OK157
macos-release-arm64OK91
macos-oldrel-arm64OK94
windows-develOK101
windows-releaseOK113
windows-oldrelOK81
wasm-releaseOK125

Exports:htc_confightc_downloadhtc_gen_executablehtc_gen_submithtc_starthtc_statushtc_submithtc_upload

Dependencies:bitbit64clicliprcpp11crayongluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readrrlangtibbletidyselecttzdbutf8vctrsvroomwithryaml

From the Notebook to the Cluster: Your First CHTC Job with submitr
The promise of a first CHTC job | The larger idea: make the right choice easy | What submitr does | Before you submit anything | A small example analysis | Step 1: configure your CHTC connection | Setting up SSH connection reuse | Step 2: generate the submit file | Step 3: generate the executable script | Step 4: preview and upload files | Step 5: submit the job | Step 6: check progress | Step 7: download results | From one test job to many HTC jobs | Where containr fits | A practical first-submission checklist | What submitr does not do | A good first goal
Rendered fromfrom-notebook-to-cluster.Rmdusingknitr::rmarkdown

Last update: 2026-05-20
Started: 2026-05-09

Single Jobs vs Multiple Jobs on HTCondor
Why two modes? | The analysis | Two kinds of manifest | Single mode: one dataset, one job | Building the container | Generating the submit file and executable | Submitting and downloading | Multiple mode: one analysis, three species | Splitting the data | Side-by-side comparison | What lives in the container | The .sub file | The .sh file | The R script | Files uploaded to the submit node | Files downloaded after the job | How htc_download() resolves files | How the two manifests relate | When to use which mode
Rendered fromsingle-vs-multiple-jobs.Rmdusingknitr::rmarkdown

Last update: 2026-05-20
Started: 2026-05-20