Package Recipe 'bioconductor-biodb'

recipe bioconductor-biodb

biodb, a library and a development framework for connecting to chemical and biological databases

Homepage:: https://bioconductor.org/packages/3.20/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.

package bioconductor-biodb¶

Versions:

1.18.0-0, 1.14.0-0, 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,

1.18.0-0, 1.14.0-0, 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:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-chk
on r-fscache >=1.0.2
on r-jsonlite
on r-lgr
on r-lifecycle
on r-openssl
on r-plyr
on r-progress
on r-r6
on r-rappdirs
on r-rcpp
on r-rsqlite
on r-sched >=1.0.1
on r-sched >=1.0.3,<1.1.0a0
on r-sqlq
on r-stringr
on r-testthat
on r-withr
on r-xml
on r-yaml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-biodb

to add into an existing workspace instead, run:

pixi add bioconductor-biodb

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-biodb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-biodb

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-biodb:<tag>

(see bioconductor-biodb/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)