recipe trimmomatic

A flexible read trimming tool for Illumina NGS data

Homepage:

http://www.usadellab.org/cms/?page=trimmomatic

License:

GPLv3

Recipe:

/trimmomatic/meta.yaml

Links:

biotools: trimmomatic, usegalaxy-eu: trimmomatic, doi: 10.1093/bioinformatics/btu170

package trimmomatic

(downloads) docker_trimmomatic

versions:
0.39-2,  0.39-1,  0.39-0,  0.38-1,  0.36-6,  0.36-5,  0.36-4,  0.36-3,  0.36-1, 

0.39-2,  0.39-1,  0.39-0,  0.38-1,  0.36-6,  0.36-5,  0.36-4,  0.36-3,  0.36-1,  0.35-7,  0.35-6,  0.35-4,  0.35-3,  0.35-2,  0.35-1,  0.33-3,  0.33-2,  0.33-1,  0.33-0,  0.32-4,  0.32-3,  0.32-2,  0.32-1,  0.32-0

depends openjdk:

depends python:

requirements:

additional platforms:

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 trimmomatic

and update with::

   mamba update trimmomatic

To create a new environment, run:

mamba create --name myenvname trimmomatic

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/trimmomatic:<tag>

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

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