recipe qcumber

Quality control, quality trimming, adapter removal and sequence content check of NGS data.

Homepage:

https://gitlab.com/RKIBioinformaticsPipelines/QCumber

License:

LGPL3

Recipe:

/qcumber/meta.yaml

package qcumber

versions:

2.0.4-0

depends bioconductor-savr:

depends bitstring:

depends bowtie2:

2.3.*

depends docopt:

depends fastqc:

0.11.*

depends jinja2:

depends kraken:

0.10.*

depends krona:

depends matplotlib:

2.0.*

depends numpy:

depends pandas:

depends python:

3.6.*

depends pyyaml:

3.12.*

depends r:

3.3.*

depends r-ggplot2:

2.2.*

depends r-quantreg:

depends r-reshape2:

depends r-stringi:

depends samtools:

1.3.*

depends seaborn:

depends setuptools:

depends snakemake:

3.12.*

depends trimmomatic:

0.36.*

depends xmltodict:

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 qcumber

and update with::

   mamba update qcumber

To create a new environment, run:

mamba create --name myenvname qcumber

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/qcumber:<tag>

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

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