{
  "_id": "6a16a35facfb0bcc41d81d07",
  "Package": "bsub",
  "Type": "Package",
  "Title": "Submitter and Monitor of the 'LSF Cluster'",
  "Version": "2.0.6",
  "Date": "2025-03-13",
  "Authors@R": "person(\"Zuguang\", \"Gu\", email = \"z.gu@dkfz.de\", role = c(\"aut\", \"cre\"),\ncomment = c('ORCID'=\"0000-0002-7395-8709\"))",
  "biocViews": "Software, Infrastructure",
  "Description": "It submits R code/R scripts/shell commands to 'LSF\ncluster' (<https://en.wikipedia.org/wiki/Platform_LSF>, the\n'bsub' system) without leaving R. There is also an interactive\n'shiny' application for monitoring job status.",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/jokergoo/bsub",
  "License": "MIT + file LICENSE",
  "NeedsCompilation": "no",
  "SystemRequirements": "Platform LSF, bsub",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "git libglpk-dev libssh-dev libssh2-1-dev\nlibxml2-dev libssl-dev perl",
  "Repository": "https://jokergoo.r-universe.dev",
  "Date/Publication": "2025-03-14 10:17:53 UTC",
  "RemoteUrl": "https://github.com/jokergoo/bsub",
  "RemoteRef": "HEAD",
  "RemoteSha": "9ae171cf7d77aa3f4f173b11ee804ce6ea447917",
  "Packaged": {
    "Date": "2026-05-27 07:52:13 UTC",
    "User": "root"
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  "Maintainer": "Zuguang Gu <z.gu@dkfz.de>",
  "MD5sum": "a84f912a8fcc6d761c0f37a641e176f3",
  "_user": "jokergoo",
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    "description": "",
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
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    "infrastructure"
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  "_stars": 27,
  "_contributors": [
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    "type": "user",
    "name": "Zuguang Gu",
    "description": "A bioinformagician"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bsub"
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
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  "_realowner": "jokergoo",
  "_cranurl": true,
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      "date": "2020-07-30"
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      "date": "2020-09-20"
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      "version": "1.1.0",
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      "date": "2025-11-28"
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      "date": "2026-04-08"
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    "bjobs",
    "bjobs_barplot",
    "bjobs_done",
    "bjobs_exit",
    "bjobs_pending",
    "bjobs_raw",
    "bjobs_reset_timestamp",
    "bjobs_running",
    "bjobs_timeline",
    "bkill",
    "brecent",
    "bsub_chunk",
    "bsub_cmd",
    "bsub_opt",
    "bsub_script",
    "config_bsub",
    "formatFileSize",
    "job_dependency_all",
    "job_dependency_diagram",
    "job_dependency_dot",
    "job_dependency_igraph",
    "job_log",
    "job_rerun",
    "job_status_by_id",
    "job_status_by_name",
    "list_dump_files",
    "list_temp_files",
    "monitor",
    "pipeline_rerun",
    "random_job",
    "remove_temp_files",
    "retrieve_var",
    "run_cmd",
    "ssh_connect",
    "ssh_disconnect"
  ],
  "_help": [
    {
      "page": "bconf",
      "title": "Print current configurations",
      "topics": [
        "bconf",
        "print.bconf"
      ]
    },
    {
      "page": "bjobs",
      "title": "Summary of jobs",
      "topics": [
        "bjobs",
        "bjobs_done",
        "bjobs_exit",
        "bjobs_pending",
        "bjobs_raw",
        "bjobs_running",
        "brecent"
      ]
    },
    {
      "page": "visualize",
      "title": "Visualize statistics of jobs",
      "topics": [
        "bjobs_barplot",
        "bjobs_timeline"
      ]
    },
    {
      "page": "bjobs_reset_timestamp",
      "title": "Clear job history",
      "topics": [
        "bjobs_reset_timestamp"
      ]
    },
    {
      "page": "bkill",
      "title": "Kill jobs",
      "topics": [
        "bkill"
      ]
    },
    {
      "page": "bsub",
      "title": "Submit jobs",
      "topics": [
        "bsub_chunk",
        "bsub_cmd",
        "bsub_script"
      ]
    },
    {
      "page": "bsub_opt",
      "title": "Parameters for bsub",
      "topics": [
        "bsub_opt"
      ]
    },
    {
      "page": "config_bsub",
      "title": "Configure bsub global options",
      "topics": [
        "config_bsub"
      ]
    },
    {
      "page": "formatFileSize",
      "title": "Format file size",
      "topics": [
        "formatFileSize"
      ]
    },
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      "topics": [
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        "job_dependency_diagram",
        "job_dependency_dot",
        "job_dependency_igraph"
      ]
    },
    {
      "page": "job_log",
      "title": "Obtain Job log",
      "topics": [
        "job_log"
      ]
    },
    {
      "page": "rerun",
      "title": "Rerun jobs",
      "topics": [
        "job_rerun",
        "pipeline_rerun"
      ]
    },
    {
      "page": "job_status",
      "title": "Job status by job ID or name",
      "topics": [
        "job_status_by_id",
        "job_status_by_name"
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    },
    {
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      "topics": [
        "list_dump_files"
      ]
    },
    {
      "page": "list_temp_files",
      "title": "Clear temporary dir",
      "topics": [
        "list_temp_files",
        "remove_temp_files"
      ]
    },
    {
      "page": "monitor",
      "title": "Browser-based interactive job monitor",
      "topics": [
        "monitor"
      ]
    },
    {
      "page": "print.bjobs",
      "title": "Summary of jobs",
      "topics": [
        "print.bjobs"
      ]
    },
    {
      "page": "random_job",
      "title": "Submit a random job",
      "topics": [
        "random_job"
      ]
    },
    {
      "page": "retrieve_var",
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      "topics": [
        "retrieve_var"
      ]
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      "page": "run_cmd",
      "title": "Run command on submission node",
      "topics": [
        "run_cmd"
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    {
      "page": "ssh",
      "title": "Connect to submisstion via ssh",
      "topics": [
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        "ssh_disconnect"
      ]
    }
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  "_readme": "https://github.com/jokergoo/bsub/raw/HEAD/README.md",
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