recipe bioconductor-mtbls2

MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/mtbls2.html

License:

CC0

Recipe:

/bioconductor-mtbls2/meta.yaml

Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites.

package bioconductor-mtbls2

(downloads) docker_bioconductor-mtbls2

Versions:
1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.27.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.1-0, 

1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.27.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.19.0-0,  1.17.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0

Depends:

  • on bioconductor-data-packages >=20260207

  • on curl

  • on r-base >=4.5,<4.6.0a0

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-mtbls2

to add into an existing workspace instead, run:

pixi add bioconductor-mtbls2

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-mtbls2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mtbls2

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-mtbls2:<tag>

(see bioconductor-mtbls2/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.

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