recipe ribotaper

RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.

Homepage:

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

License:

GPL-3.0-or-later

Recipe:

/ribotaper/meta.yaml

Links:

biotools: ribotaper, doi: 10.1038/nmeth.3688

package ribotaper

versions:

1.3.1-0,  1.3.1a-8,  1.3.1a-7,  1.3.1a-6,  1.3.1a-5,  1.3.1a-4,  1.3.1a-3,  1.3.1a-2,  1.3.1a-1, 

1.3.1-0,  1.3.1a-8,  1.3.1a-7,  1.3.1a-6,  1.3.1a-5,  1.3.1a-4,  1.3.1a-3,  1.3.1a-2,  1.3.1a-1,  1.3.1a-0

depends bedtools:

==2.17.0

depends r-ade4:

depends r-domc:

depends r-foreach:

depends r-iterators:

depends r-multitaper:

depends r-seqinr:

depends r-xnomial:

depends samtools:

requirements:

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 ribotaper

and update with::

   mamba update ribotaper

To create a new environment, run:

mamba create --name myenvname ribotaper

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/ribotaper:<tag>

(see `ribotaper/tags`_ for valid values for ``<tag>``)

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