recipe bactopia-qc

The methods used in Bactopia for read QC

Homepage:

https://bactopia.github.io/

Developer docs:

https://github.com/bactopia/bactopia-qc/

License:

MIT

Recipe:

/bactopia-qc/meta.yaml

Links:

biotools: bactopia, doi: 10.1128/mSystems.00190-20

package bactopia-qc

versions:

1.0.2-0,  1.0.1-0,  1.0.0-0

depends bbmap:

>=39.01

depends biopython:

1.77.*

depends coreutils:

depends fastp:

>=0.23.4

depends fastq-scan:

>=1.0.1

depends fastqc:

>=0.12.1

depends gsl:

2.6.*

depends lighter:

>=1.1.2

depends nanoplot:

>=1.41.6

depends nanoq:

>=0.10.0

depends pigz:

depends porechop:

>=0.2.4

depends python:

>=3.7,<3.11

depends rasusa:

>=0.7.1

depends rename:

depends sed:

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 bactopia-qc

and update with::

   mamba update bactopia-qc

To create a new environment, run:

mamba create --name myenvname bactopia-qc

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/bactopia-qc:<tag>

(see `bactopia-qc/tags`_ for valid values for ``<tag>``)

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