Package: condathis 0.0.3.9023

condathis: Condathis: run any CLI tool on a Conda Environment

Condathis is an R package that simplifies the execution of command line tools within isolated conda environments. It enables users to effortlessly manage Conda environments, execute command line tools, handle dependencies, and ensure reproducibility in their data analysis workflows.

Authors:Lucio Rezende Queiroz [aut, cre]

condathis_0.0.3.9023.tar.gz
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condathis.pdf |condathis.html✨
condathis/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/luciorq/condathis/issues

On CRAN:

bioinformaticscondareproducibilityreproducible-research

12 exports 3 stars 1.16 score 15 dependencies 2 scripts

Last updated 5 days agofrom:052898d85a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:build_container_imagecreate_envenv_existsget_install_dirget_sys_archinstall_micromambainstall_packageslist_envslist_packagesmicromamba_bin_pathremove_envrun

Dependencies:clifsgluejsonlitelifecyclemagrittrprocessxpsR6rappdirsrlangstringistringrvctrswithr

Readme and manuals

Help Manual

Help pageTopics
Build Micromamba Container Imagebuild_container_image
Build Singularity / Apptainer Imagebuild_container_image_singularity
Create a Conda Environmentcreate_env
Create Environment Using Dockercreate_env_internal_docker
Create Environment Using Singularity / Apptainercreate_env_internal_singularity
Automatically Find Suitable Infrastrucure to Run CLI Toolsdefine_method_to_use
Define Platform to be used by 'create_env()'.define_platform
Check If Environment Names Already existsenv_exists
Format Channels Argumentsformat_channels_args
Format user string for Dockerformat_user_arg_string
Retrieve 'condathis' Data Creation Pathget_install_dir
Return OS and CPU Architectureget_sys_arch
Install Micromamba binaries in a 'condathis' controlled path.install_micromamba
Install Packages in a Existing Conda Environmentinstall_packages
Check If Command Line Tool Is Availableis_cmd_available
Check if Micromamba is Available for OS and CPU architectureis_micromamba_available_for_arch
Are Singularity or Apptainer CLIs availableis_singularity_available
List Installed Environmentslist_envs
List Packages Installed Inside Environmentlist_packages
Retrieve the path to the 'condathis' managed installation of 'micromamba'.micromamba_bin_path
Retrieve Micromamba Installed Pathmicromamba_user_installed
Run Micromamba Commandnative_cmd
Search for Packages in Channels using Dockerpackages_search_docker
Search For Package in Channelspackages_search_native
Search for packages in Channels using Singularitypackages_search_singularity
Remove a Conda Environmentremove_env
Run Command Line tools in a Conda environment.run
Stop execution if 'dockerthis' package is not installed.stop_if_not_installed