- recipe sneakernet-qc
A QC pipeline for raw reads
- Homepage:
- License:
MIT
- Recipe:
- Links:
doi: 10.21105/joss.02334
- package sneakernet-qc¶
- Versions:
0.27.2-0,0.27.0-1,0.27.0-0,0.26.0-0,0.25.0-0- Depends:
on blast
on bowtie2
on chewbbaca
on colorid_bv
on fastqc
on flash
on kalamari
on kma
>=1.4on kmc
on kraken
>=1,<2on krona
on lighter
on make
on mash
>=2on megahit
on mlst
on multiqc
on perl
>=5.32.1,<6.0a0 *_perl5on perl-app-cpanminus
on perl-bioperl
on perl-config-simple
on perl-file-slurp
on perl-gd
on perl-gdgraph
on perl-list-moreutils
on perl-moo
on perl-statistics-descriptive
on perl-text-levenshtein
>=0.15on pilon
on prodigal
on python
>=3.7on quast
on salmid
on samclip
on seqtk
on shovill
on skesa
>=2.4on spades
on staramr
on trimmomatic
- 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 sneakernet-qc
to add into an existing workspace instead, run:
pixi add sneakernet-qc
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 sneakernet-qc
Alternatively, to install into a new environment, run:
conda create -n envname sneakernet-qc
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/sneakernet-qc:<tag>
(see sneakernet-qc/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/sneakernet-qc/README.html)
