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:

0.0.5-0,  0.0.4-1,  0.0.4-0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-msa2dist:

>=1.6.0,<1.7.0a0

depends last:

>=1542

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-curl:

depends r-devtools:

depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-gridextra:

depends r-knitr:

depends r-markdown:

depends r-readr:

depends r-rlang:

depends r-seqinr:

depends r-stringi:

depends r-stringr:

depends r-testthat:

depends r-tibble:

depends r-tidyr:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-crbhits

and update with::

   mamba update r-crbhits

To create a new environment, run:

mamba create --name myenvname r-crbhits

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-crbhits:<tag>

(see `r-crbhits/tags`_ for valid values for ``<tag>``)

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