recipe ngs_te_mapper2

A program to identify transposable element insertions using next generation sequencing data.

Homepage:

https://github.com/bergmanlab/ngs_te_mapper2

License:

BSD

Recipe:

/ngs_te_mapper2/meta.yaml

package ngs_te_mapper2

versions:

1.0.2-1,  1.0.2-0

depends bcftools:

depends bedtools:

depends biopython:

depends bwa:

depends minimap2:

depends numpy:

depends pip:

depends pysam:

depends python:

>=3.6

depends repeatmasker:

4.0.7.*

depends samtools:

>=1.9

depends seqtk:

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 ngs_te_mapper2

and update with::

   mamba update ngs_te_mapper2

To create a new environment, run:

mamba create --name myenvname ngs_te_mapper2

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/ngs_te_mapper2:<tag>

(see `ngs_te_mapper2/tags`_ for valid values for ``<tag>``)

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Link to this page

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