recipe fastp

A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting…).

Homepage:

https://github.com/OpenGene/fastp

Documentation:

https://github.com/OpenGene/fastp/blob/v0.24.1/README.md

License:

MIT / MIT

Recipe:

/fastp/meta.yaml

Links:

biotools: fastp, usegalaxy-eu: fastp, doi: 10.1002/imt2.107

package fastp

(downloads) docker_fastp

versions:
0.24.1-0,  0.24.0-1,  0.24.0-0,  0.23.4-5,  0.23.4-4,  0.23.4-3,  0.23.4-2,  0.23.4-1,  0.23.4-0, 

0.24.1-0,  0.24.0-1,  0.24.0-0,  0.23.4-5,  0.23.4-4,  0.23.4-3,  0.23.4-2,  0.23.4-1,  0.23.4-0,  0.23.3-0,  0.23.2-5,  0.23.2-4,  0.23.2-3,  0.23.2-2,  0.23.2-1,  0.23.2-0,  0.23.1-0,  0.23.0-0,  0.22.0-0,  0.20.1-1,  0.20.1-0,  0.20.0-0,  0.19.7-0,  0.19.6-0,  0.19.5-0,  0.19.4-0,  0.19.3-0,  0.18.0-0,  0.17.1-0,  0.17.0-0,  0.14.1-0,  0.13.1-0,  0.12.5-0,  0.12.4-0,  0.12.3-0,  0.12.2-1,  0.12.2-0

depends isa-l:

>=2.31.1,<3.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 fastp

and update with::

   mamba update fastp

To create a new environment, run:

mamba create --name myenvname fastp

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/fastp:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/fastp/README.html)