:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-biodb' .. highlight: bash bioconductor-biodb ================== .. conda:recipe:: bioconductor-biodb :replaces_section_title: :noindex: biodb\, a library and a development framework for connecting to chemical and biological databases :homepage: https://bioconductor.org/packages/3.18/bioc/html/biodb.html :license: AGPL-3 :recipe: /`bioconductor-biodb `_/`meta.yaml `_ The biodb package provides access to standard remote chemical and biological databases \(ChEBI\, KEGG\, HMDB\, ...\)\, as well as to in\-house local database files \(CSV\, SQLite\)\, with easy retrieval of entries\, access to web services\, search of compounds by mass and\/or name\, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages. .. conda:package:: bioconductor-biodb |downloads_bioconductor-biodb| |docker_bioconductor-biodb| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.2.2-1``,  ``1.2.2-0``,  ``1.2.0-0``,  ``1.0.3-0`` :depends bioconductor-biocfilecache: ``>=2.10.0,<2.11.0`` :depends bioconductor-biocfilecache: ``>=2.10.1,<2.11.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-chk: :depends r-git2r: :depends r-jsonlite: :depends r-lgr: :depends r-lifecycle: :depends r-openssl: :depends r-plyr: :depends r-progress: :depends r-r6: :depends r-rappdirs: :depends r-rcpp: :depends r-rcurl: :depends r-rsqlite: :depends r-stringr: :depends r-testthat: :depends r-withr: :depends r-xml: :depends r-yaml: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-biodb and update with:: mamba update bioconductor-biodb To create a new environment, run:: mamba create --name myenvname bioconductor-biodb with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-biodb: (see `bioconductor-biodb/tags`_ for valid values for ````) .. |downloads_bioconductor-biodb| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-biodb.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-biodb :alt: (downloads) .. |docker_bioconductor-biodb| image:: https://quay.io/repository/biocontainers/bioconductor-biodb/status :target: https://quay.io/repository/biocontainers/bioconductor-biodb .. _`bioconductor-biodb/tags`: https://quay.io/repository/biocontainers/bioconductor-biodb?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biodb/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-biodb/README.html