recipe xtea

TE insertion caller for both short and long reads

Homepage:

https://github.com/parklab/xTea

License:

Academic and Non-Commercial Research Use

Recipe:

/xtea/meta.yaml

package xtea

versions:

0.1.9-0,  0.1.8-0,  0.1.7-0,  0.1.6-0,  0.1.5-0,  0.1.4-0,  0.1.3-0,  0.1.2-0

depends bwa:

>=0.7.17

depends minimap2:

depends numpy:

depends pandas:

depends pysam:

>=0.15.0

depends python:

depends samtools:

>=1.0

depends scikit-learn:

0.20.0

depends sortedcontainers:

depends wtdbg:

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 xtea

and update with::

   mamba update xtea

To create a new environment, run:

mamba create --name myenvname xtea

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/xtea:<tag>

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

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Link to this page

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