recipe r-rphast

Provides an R interface to the 'PHAST'(<http://compgen.cshl.edu/phast/>) software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.

Homepage:

https://github.com/CshlSiepelLab/RPHAST

Documentation:

http://compgen.cshl.edu/phast

License:

BSD / BSD-3-Clause

Recipe:

/r-rphast/meta.yaml

package r-rphast

(downloads) docker_r-rphast

Versions:
1.6.11-1,  1.6.11-0,  1.6.9-9,  1.6.9-8,  1.6.9-7,  1.6.9-6,  1.6.9-5,  1.6.9-4,  1.6.9-3, 

1.6.11-1,  1.6.11-0,  1.6.9-9,  1.6.9-8,  1.6.9-7,  1.6.9-6,  1.6.9-5,  1.6.9-4,  1.6.9-3,  1.6.9-2,  1.6.9-1,  1.6.9-0

Depends:

  • on blis >=0.9.0

  • on libgcc >=13

  • on liblapack >=3.9.0,<4.0a0

  • on pcre >=8.45,<9.0a0

  • on r-base >=4.5,<4.6.0a0

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-rphast

to add into an existing workspace instead, run:

pixi add r-rphast

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-rphast

Alternatively, to install into a new environment, run:

conda create -n envname r-rphast

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-rphast:<tag>

(see r-rphast/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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