recipe edta

Extensive de-novo TE Annotator.

Homepage:

https://github.com/oushujun/EDTA

Documentation:

https://github.com/oushujun/EDTA/wiki

License:

GPL3 / GPL-3.0-only

Recipe:

/edta/meta.yaml

Links:

doi: 10.1186/s13059-019-1905-y, doi: 10.1101/2022.10.09.511471, biotools: EDTA, usegalaxy-eu: edta

package edta

versions:

2.2.2-1,  2.2.2-0,  2.2.0-1,  2.2.0-0,  2.1.0-1,  2.1.0-0,  2.0.1-0,  2.0.0-0,  1.9.6-2, 

2.2.2-1,  2.2.2-0,  2.2.0-1,  2.2.0-0,  2.1.0-1,  2.1.0-0,  2.0.1-0,  2.0.0-0,  1.9.6-2,  1.9.6-1,  1.9.6-0,  1.9.5-0,  1.9.4-0,  1.9.0-1,  1.9.0-0,  1.8.3-0,  1.8.2-0,  1.7.8-0,  1.7.7-0

depends annosine2:

depends bedtools:

depends biopython:

depends cd-hit:

depends coreutils:

depends genometools-genometools:

depends grep:

depends helitronscanner:

depends ltr_finder_parallel:

depends ltr_harvest_parallel:

depends ltr_retriever:

>=3.0.0

depends mdust:

depends muscle:

depends openjdk:

depends pandas:

depends perl:

depends perl-json:

depends perl-text-soundex:

depends pyarrow:

depends python:

>=3.8

depends r-base:

depends r-dplyr:

depends r-ggplot2:

depends r-here:

depends r-tidyr:

depends repeatmasker:

depends repeatmodeler:

>=2

depends samtools:

depends tesorter:

depends tir-learner:

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 edta

and update with::

   mamba update edta

To create a new environment, run:

mamba create --name myenvname edta

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/edta:<tag>

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

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