Package Recipe 'bioconductor-msa'

recipe bioconductor-msa

Multiple Sequence Alignment

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/msa.html
License:: GPL (>= 2)
Recipe:: /bioconductor-msa/meta.yaml
Links:: biotools: msa

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

package bioconductor-msa¶

Versions:

1.42.0-0, 1.38.0-0, 1.34.0-1, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.26.0-2, 1.26.0-1,

1.42.0-0, 1.38.0-0, 1.34.0-1, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.26.0-2, 1.26.0-1, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.14.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc
on libgcc-ng >=12
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx
on libstdcxx-ng >=12
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-rcpp >=0.11.1

Additional platforms:

linux-aarch64

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-msa

to add into an existing workspace instead, run:

pixi add bioconductor-msa

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-msa

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-msa

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-msa:<tag>

(see bioconductor-msa/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-msa/README.html)