recipe humanfilt

WGS human-read filtering with auto-downloaded human references

Homepage:

https://github.com/jprehn-lab/humanfilt

License:

MIT

Recipe:

/humanfilt/meta.yaml

package humanfilt

versions:

0.1.1-0

depends bbmap:

depends bowtie2:

depends bwa:

depends fastuniq:

depends kraken2:

depends minimap2:

depends pigz:

depends python:

>=3.10

depends samtools:

depends seqkit:

depends trim-galore:

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 humanfilt

and update with::

   mamba update humanfilt

To create a new environment, run:

mamba create --name myenvname humanfilt

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/humanfilt:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

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