recipe lofreq

A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data

Homepage:

http://csb5.github.io/lofreq/

License:

MIT

Recipe:

/lofreq/meta.yaml

Links:

usegalaxy-eu: lofreq_call

package lofreq

(downloads) docker_lofreq

versions:
2.1.5-102.1.5-92.1.5-82.1.5-72.1.5-62.1.5-52.1.5-42.1.5-32.1.5-2

2.1.5-102.1.5-92.1.5-82.1.5-72.1.5-62.1.5-52.1.5-42.1.5-32.1.5-22.1.5-12.1.5-02.1.4-32.1.4-22.1.3.1-02.1.2-0

depends htslib:

>=1.17,<1.20.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

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 lofreq

and update with::

   mamba update lofreq

To create a new environment, run:

mamba create --name myenvname lofreq

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/lofreq:<tag>

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

Download stats