recipe te-aid

Annotation helper tool for the manual curation of transposable element consensus sequences

Homepage:

https://github.com/clemgoub/TE-Aid/tree/v{version}

Developer docs:

https://github.com/clemgoub/TE-Aid

License:

MIT

Recipe:

/te-aid/meta.yaml

TE-Aid is a shell+R program aimed to help the manual curation of transposable elements (TE). It inputs a TE consensus sequence (fasta format) and requires a reference genome (in fasta as well). TE-Aid produces 4 figures reporting i) the genomic hits with divergence to consensus, ii) the genomic coverage of the consensus, iii) a self dot-plot, and iv) a structure analysis including TIR and LTR suggestions, open reading frames (ORFs) and TE protein hit annotation.

package te-aid

(downloads) docker_te-aid

versions:

1.0.0-0

depends bioconductor-biostrings:

>=2.70.1

depends blast:

>=2.15.0

depends emboss:

>=6.6.0

depends r:

>=4.2

depends r-rcpp:

>=1.0.12

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 te-aid

and update with::

   mamba update te-aid

To create a new environment, run:

mamba create --name myenvname te-aid

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/te-aid:<tag>

(see `te-aid/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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