recipe fastq_utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Homepage:

https://github.com/nunofonseca/fastq_utils

License:

GPL / GPL-3.0-only

Recipe:

/fastq_utils/meta.yaml

package fastq_utils

versions:

0.25.2-2,  0.25.2-1,  0.25.2-0,  0.25.1-1,  0.25.1-0,  0.24.1-1,  0.24.1-0,  0.24.0-0,  0.23.0-0, 

0.25.2-2,  0.25.2-1,  0.25.2-0,  0.25.1-1,  0.25.1-0,  0.24.1-1,  0.24.1-0,  0.24.0-0,  0.23.0-0,  0.22.1-0,  0.22.0-0,  0.21.0-0,  0.20.0-0,  0.19.3-0,  0.19.2-0,  0.18.2-1

depends libgcc:

>=13

depends libzlib:

>=1.2.13,<2.0a0

depends ncurses:

>=6.5,<7.0a0

depends samtools:

depends zlib:

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 fastq_utils

and update with::

   mamba update fastq_utils

To create a new environment, run:

mamba create --name myenvname fastq_utils

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_utils:<tag>

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

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