- recipe tetrimmer
TETrimmer is designed to replace and assist TE manual curation.
- Homepage:
- License:
GPL3 / GPL-3.0-only
- Recipe:
- package tetrimmer¶
- versions:
1.4.0-0- depends bedtools:
>=2.31.1- depends biopython:
- depends blast:
- depends cd-hit:
- depends click:
- depends dataclasses:
- depends dill:
- depends emboss:
- depends ghostscript:
- depends hmmer:
- depends iqtree:
- depends joblib:
- depends mafft:
- depends matplotlib-base:
- depends multiprocess:
- depends nseg:
- depends numpy:
- depends pandas:
- depends perl:
- depends pfam_scan:
- depends plotly:
- depends pypdf2:
- depends python:
>=3.8,<3.11- depends r-base:
- depends recon:
- depends regex:
- depends repeatmasker:
- depends repeatmodeler:
- depends requests:
- depends samtools:
- depends scikit-learn:
- depends tk:
- depends trf:
- depends urllib3:
- 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 tetrimmer and update with:: mamba update tetrimmer
To create a new environment, run:
mamba create --name myenvname tetrimmer
with
myenvnamebeing 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/tetrimmer:<tag> (see `tetrimmer/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/tetrimmer/README.html)
