recipe fastq

A simple FASTQ toolbox for small to medium size projects without dependencies.

Homepage:

https://github.com/not-a-feature/fastq

License:

GPL3 / GPL-3.0-or-later

Recipe:

/fastq/meta.yaml

FASTQ files are text-based files for storing nucleotide sequences and its corresponding quality scores. Reading such files is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies. fastq offers an alternative to this and brings many useful functions without relying on third party packages.

package fastq

versions:

2.0.4-0,  2.0.2-0,  2.0.1-0,  1.2.2-0

depends minifasta:

>=3.0.1

depends python:

>=3.8

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 fastq

and update with::

   mamba update fastq

To create a new environment, run:

mamba create --name myenvname fastq

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/fastq:<tag>

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

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