recipe bioconductor-basecallqc

Working with Illumina Basecalling and Demultiplexing input and output files

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/basecallQC.html

License:

GPL (>= 3)

Recipe:

/bioconductor-basecallqc/meta.yaml

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

package bioconductor-basecallqc

versions:

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0, 

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-knitr:

depends r-lazyeval:

depends r-magrittr:

depends r-prettydoc:

depends r-raster:

depends r-rmarkdown:

depends r-stringr:

depends r-tidyr:

depends r-xml:

depends r-yaml:

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 bioconductor-basecallqc

and update with::

   mamba update bioconductor-basecallqc

To create a new environment, run:

mamba create --name myenvname bioconductor-basecallqc

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/bioconductor-basecallqc:<tag>

(see `bioconductor-basecallqc/tags`_ for valid values for ``<tag>``)

Notes

'This package relies on bcl2fastq being available in the system PATH. Due to licensing restrictions Bioconda does not provide this package.'

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