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:

2.2.0-1,  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, 

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 blast:

depends cd-hit:

depends coreutils:

depends genericrepeatfinder:

depends genometools-genometools:

depends glob2:

depends h5py:

depends hmmer:

depends irfinder:

depends keras:

depends ltr_finder:

depends ltr_retriever:

depends matplotlib-base:

depends mdust:

depends minimap2:

depends multiprocess:

depends muscle:

depends nodejs:

depends openjdk:

depends pandas:

depends perl:

depends perl-text-soundex:

depends python:

>=3.8

depends regex:

depends repeatmodeler:

depends scikit-learn:

depends seqtk:

depends swifter:

depends tensorflow:

depends tesorter:

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 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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