Package: Capsule 0.2.0

Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

A comprehensive reproducibility framework designed for R and bioinformatics workflows. Automatically captures the entire analysis environment including R session info, package versions, external tool versions (Samtools, STAR, BWA, etc.), conda environments, reference genomes, data provenance with smart checksumming for large files, parameter choices, random seeds, and hardware specifications. Generates executable scripts with Docker, Singularity, and renv configurations. Integrates with workflow managers (Nextflow, Snakemake, WDL, CWL) to ensure complete reproducibility of computational research workflows.

Authors:Abu SAADAT [aut, cre]

Capsule_0.2.0.tar.gz
Capsule_0.2.0.zip(r-4.7)Capsule_0.2.0.zip(r-4.6)Capsule_0.2.0.zip(r-4.5)
Capsule_0.2.0.tgz(r-4.6-any)Capsule_0.2.0.tgz(r-4.5-any)
Capsule_0.2.0.tar.gz(r-4.7-any)Capsule_0.2.0.tar.gz(r-4.6-any)
Capsule_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Capsule/json (API)
NEWS

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

Bug tracker:https://github.com/saadat-abu/capsule/issues

On CRAN:

Conda:

4.36 score 7 stars 22 scripts 144 downloads 34 exports 5 dependencies

Last updated from:5d47c2cde3. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE172
source / vignettesOK271
linux-release-x86_64NOTE125
macos-release-arm64NOTE117
macos-oldrel-arm64NOTE185
windows-develNOTE82
windows-releaseNOTE67
windows-oldrelNOTE62
wasm-releaseOK92

Exports:capture_environmentcapture_hardwarecapture_sessioncapture_system_librariescompare_snapshotscreate_renv_lockfilecreate_repro_reportexport_for_cwlexport_for_nextflowexport_for_snakemakeexport_for_wdlgenerate_dockergenerate_repro_scriptgenerate_singularityget_conda_env_infoget_data_lineageget_param_historyget_reference_infoget_seed_historyget_tool_versionsinit_capsulelist_reference_sourceslist_snapshotsrestore_conda_envrestore_seedset_seedsnapshot_packagessnapshot_workflowtrack_conda_envtrack_datatrack_external_toolstrack_paramstrack_reference_genomeverify_data

Dependencies:clidigestjsonliterenvyaml

Readme and manuals

Help Manual

Help pageTopics
Capture Environment Statecapture_environment
Capture Hardware Informationcapture_hardware
Capture Complete Session Informationcapture_session
Capture System Librariescapture_system_libraries
Compare Two Workflow Snapshotscompare_snapshots
Create renv Lockfilecreate_renv_lockfile
Create Reproducibility Reportcreate_repro_report
Generate CWL (Common Workflow Language) Inputexport_for_cwl
Export Capsule Data for Nextflowexport_for_nextflow
Export Capsule Data for Snakemakeexport_for_snakemake
Create WDL (Workflow Description Language) Configexport_for_wdl
Generate Docker Configurationgenerate_docker
Generate Reproducible Scriptgenerate_repro_script
Generate Singularity Definition Filegenerate_singularity
Get Conda Environment Infoget_conda_env_info
Get Data Lineageget_data_lineage
Get Parameter Historyget_param_history
Get Reference Genome Informationget_reference_info
Get Seed Historyget_seed_history
Get External Tool Versionsget_tool_versions
Initialize Capsule in Projectinit_capsule
List Common Reference Genome Sourceslist_reference_sources
List Available Snapshotslist_snapshots
Restore Conda Environmentrestore_conda_env
Restore Random Seedrestore_seed
Set and Track Random Seedset_seed
Track Package Versions and Dependenciessnapshot_packages
Create Complete Workflow Snapshotsnapshot_workflow
Track Conda Environmenttrack_conda_env
Track Data Provenancetrack_data
Track External Bioinformatics Toolstrack_external_tools
Track Analysis Parameterstrack_params
Track Reference Genometrack_reference_genome
Verify Data Integrityverify_data