├── .Rbuildignore ├── .circleci └── config.yml ├── .editorconfig ├── .gitignore ├── BioInstaller.Rproj ├── ChangeLog ├── DESCRIPTION ├── Dockerfile ├── LICENSE ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── BioInstaller.R ├── active.R ├── conda.R ├── config.R ├── crawl.R ├── docker.R ├── info.R ├── install.R ├── install_utils.R ├── meta.R ├── spack.R ├── utils_function.R └── versions.R ├── README.md ├── _pkgdown.yml ├── inst └── extdata │ ├── config │ ├── db │ │ ├── db_annovar.toml │ │ ├── db_blast.toml │ │ ├── db_main.toml │ │ ├── db_meta.toml │ │ └── db_ucsc.toml.gz │ ├── docker │ │ └── docker.toml │ ├── github │ │ ├── github.toml │ │ └── github_meta.toml │ ├── nongithub │ │ ├── nongithub.toml │ │ └── nongithub_meta.toml │ └── web │ │ └── web_meta.toml │ ├── demo │ └── softwares_db_demo.yaml │ ├── files │ └── sedb_files │ ├── scripts │ ├── echo_root_env.sh │ ├── install.R │ ├── install_tvc.sh │ └── parse_version.R │ └── sql │ ├── output_file_table.sql │ ├── task_table.sql │ └── upload_table.sql ├── man ├── BioInstaller.Rd ├── change.info.Rd ├── conda.Rd ├── conda.env.create.Rd ├── conda.env.list.Rd ├── conda.list.Rd ├── crawl.all.versions.Rd ├── del.info.Rd ├── docker.pull.Rd ├── docker.search.Rd ├── figures │ ├── design_of_bioInstaller.jpg │ ├── logo.png │ └── logo.svg ├── get.info.Rd ├── get.meta.Rd ├── get.meta.files.Rd ├── install.bioinfo.Rd ├── install.github.Rd ├── install.nongithub.Rd ├── is.biosoftwares.db.active.Rd ├── new.bioinfo.Rd ├── set.biosoftwares.db.Rd ├── show.installed.Rd ├── spack.Rd └── spack.list.Rd ├── tests ├── testthat.R └── testthat │ ├── test_active.R │ ├── test_docker.R │ ├── test_info.R │ ├── test_install.R │ ├── test_install_utils.R │ ├── test_meta.R │ ├── test_utils.R │ └── test_versions.R └── vignettes ├── BioInstaller.Rmd ├── download.Rmd ├── items_description.Rmd ├── plugins_of_bioshiny.Rmd ├── start_bioshiny.Rmd └── write_configuration_file.Rmd /.Rbuildignore: 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