Package Recipe 'adtoolbox' — Bioconda documentation

recipe adtoolbox

Modeling and optimization of anaerobic digestion, from sequencing reads to ADM1/e-ADM simulation

Homepage:: chan-csu/ADToolbox
Documentation:: https://chan-csu.github.io/ADToolbox/
License:: MIT / MIT
Recipe:: /adtoolbox/meta.yaml

ADToolbox turns metagenomics evidence into model-ready anaerobic digestion simulations. It maps 16S amplicon data through GTDB and a curated enzyme-to-reaction database, or profiles shotgun reads directly, to produce the microbial COD allocation an extended ADM (e-ADM) model needs -- then simulates, visualizes, and calibrates the model against experimental data.

package adtoolbox#

Versions:

1.1.16-0

Depends:

on bioconductor-dada2
on click >=8.1.7
on cutadapt
on fastp
on mmseqs2
on nbformat >=4.2.0
on ncbi-datasets-cli
on numpy >=1.22.4
on plotly >=5.8.0
on polars >=0.20.27
on python >=3.11
on requests >=2.27.1
on rich >=12.4.4
on scipy >=1.8.1
on sra-tools
on vsearch

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 adtoolbox

to add into an existing workspace instead, run:

pixi add adtoolbox

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 adtoolbox

Alternatively, to install into a new environment, run:

conda create -n envname adtoolbox

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/adtoolbox:<tag>

(see adtoolbox/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/adtoolbox/README.html)