recipe elprep

elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.

Homepage:

https://github.com/ExaScience/elprep

License:

AGPL / AGPL-3.0-only

Recipe:

/elprep/meta.yaml

Links:

biotools: Elprep, doi: 10.1371/journal.pone.0244471

package elprep

(downloads) docker_elprep

versions:
5.1.3-1,  5.1.3-0,  5.1.2-0,  5.1.1-0,  5.1.0-0,  5.0.2-0,  5.0.1-1,  5.0.1-0,  4.1.6-1, 

5.1.3-1,  5.1.3-0,  5.1.2-0,  5.1.1-0,  5.1.0-0,  5.0.2-0,  5.0.1-1,  5.0.1-0,  4.1.6-1,  4.1.6-0,  4.1.5-0,  4.1.4-0,  4.1.3-0,  4.1.2-0,  4.1.1-0,  4.1.0-0,  4.0.1-0,  4.0.0-0,  3.04-1,  3.04-0

requirements:

additional platforms:
linux-aarch64

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 elprep

and update with::

   mamba update elprep

To create a new environment, run:

mamba create --name myenvname elprep

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/elprep:<tag>

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

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