Package Recipe 'r-crbhits'

recipe r-crbhits

CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R.

Homepage:: https://github.com/kullrich/CRBHits
License:: MIT / MIT
Recipe:: /r-crbhits/meta.yaml
Links:: doi: 10.21105/joss.02424

CRBHits is a reimplementation of the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast in R. It covers all necessary steps from CRBHit pair calculation to Codon Alignments and Ka/Ks. (see [Ullrich (2020) <https://doi.org/10.21105/joss.02424>])

package r-crbhits¶

Versions:

0.0.7-1, 0.0.7-0, 0.0.5-0, 0.0.4-1, 0.0.4-0

Depends:

on bioconductor-biostrings >=2.74.0,<2.75.0a0
on bioconductor-msa2dist >=1.10.0,<1.11.0a0
on dagchainer >=0r.120920
on kakscalculator2 >=2.0.1,<3.0a0
on last >=1608
on libgcc >=13
on libstdcxx >=13
on r-ape
on r-base >=4.4,<4.5.0a0
on r-curl
on r-devtools
on r-doparallel
on r-dplyr
on r-foreach
on r-ggplot2
on r-gridextra
on r-knitr
on r-markdown
on r-readr
on r-rlang
on r-seqinr
on r-stringi
on r-stringr
on r-testthat
on r-tibble
on r-tidyr

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 r-crbhits

to add into an existing workspace instead, run:

pixi add r-crbhits

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 r-crbhits

Alternatively, to install into a new environment, run:

conda create -n envname r-crbhits

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/r-crbhits:<tag>

(see r-crbhits/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:

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