- recipe qcumber
Quality control, quality trimming, adapter removal and sequence content check of NGS data.
- Homepage:
- License:
LGPL3
- Recipe:
- package qcumber¶
- Versions:
2.0.4-0- Depends:
on bioconductor-savr
on bitstring
on bowtie2
2.3.*on docopt
on fastqc
0.11.*on jinja2
on kraken
0.10.*on krona
on matplotlib
2.0.*on numpy
on pandas
on python
3.6.*on pyyaml
3.12.*on r
3.3.*on r-ggplot2
2.2.*on r-quantreg
on r-reshape2
on r-stringi
on samtools
1.3.*on seaborn
on setuptools
on snakemake
3.12.*on trimmomatic
0.36.*on xmltodict
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install qcumber
to add into an existing workspace instead, run:
pixi add qcumber
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install qcumber
Alternatively, to install into a new environment, run:
conda create -n envname qcumber
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/qcumber:<tag>
(see qcumber/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/qcumber/README.html)
