recipe tir-learner

An ensemble pipeline for terminal inverted repeat (TIR) transposable elements annotation.

Homepage:

https://github.com/lutianyu2001/TIR-Learner

Documentation:

https://github.com/lutianyu2001/TIR-Learner/blob/main/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/tir-learner/meta.yaml

Links:

doi: 10.6084/m9.figshare.26082574.v1

package tir-learner

versions:

3.0.3-1,  3.0.3-0,  3.0.2-1,  3.0.2-0,  3.0.1-0

depends biopython:

depends genericrepeatfinder:

depends genometools-genometools:

depends keras:

>=3.3.3

depends multiprocess:

depends pandas:

depends pytorch:

depends regex:

depends rmblast:

depends scikit-learn:

>=1.3

depends swifter:

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 tir-learner

and update with::

   mamba update tir-learner

To create a new environment, run:

mamba create --name myenvname tir-learner

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/tir-learner:<tag>

(see `tir-learner/tags`_ for valid values for ``<tag>``)

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