recipe sneakernet-qc

A QC pipeline for raw reads

Homepage:

https://github.com/lskatz/sneakernet

License:

MIT

Recipe:

/sneakernet-qc/meta.yaml

Links:

doi: 10.21105/joss.02334

package sneakernet-qc

versions:

0.27.0-1,  0.27.0-0,  0.26.0-0,  0.25.0-0

depends blast:

depends bowtie2:

depends chewbbaca:

depends colorid_bv:

depends fastqc:

depends flash:

depends kalamari:

depends kma:

>=1.4

depends kmc:

depends kraken:

>=1,<2

depends krona:

depends lighter:

depends make:

depends mash:

>=2

depends megahit:

depends mlst:

depends multiqc:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-app-cpanminus:

depends perl-bioperl:

depends perl-cg-pipeline:

depends perl-config-simple:

depends perl-file-slurp:

depends perl-gd:

depends perl-gdgraph:

depends perl-list-moreutils:

depends perl-moo:

depends perl-statistics-descriptive:

depends perl-text-levenshtein:

>=0.15

depends pilon:

depends prodigal:

depends python:

>=3.7

depends quast:

depends salmid:

depends samclip:

depends seqtk:

depends shovill:

depends skesa:

>=2.4

depends spades:

depends staramr:

depends trimmomatic:

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 sneakernet-qc

and update with::

   mamba update sneakernet-qc

To create a new environment, run:

mamba create --name myenvname sneakernet-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/sneakernet-qc:<tag>

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

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