recipe telr

A a fast non-reference transposable element (TE) detector from long read (LR) sequencing data (PacBio or Oxford Nanopore).

Homepage:

https://github.com/bergmanlab/telr

License:

BSD-2-Clause

Recipe:

/telr/meta.yaml

package telr

versions:

1.1-0,  0.2-2,  0.2-1,  0.2-0

depends bcftools:

1.9.*

depends bedtools:

depends biopython:

depends flye:

depends minimap2:

depends ngmlr:

depends numpy:

depends pandas:

>=1.0.0

depends pip:

depends pysam:

>=0.15

depends python:

>=3.6

depends repeatmasker:

4.0.7.*

depends rmblast:

2.6.0.*

depends samtools:

1.9.*

depends seqtk:

depends sniffles:

1.0.12.*

depends wtdbg:

>=2.5

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 telr

and update with::

   mamba update telr

To create a new environment, run:

mamba create --name myenvname telr

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/telr:<tag>

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

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