recipe sequenoscope

sequenoscope is a versatile bioinformatic pipeline for the analysis of sequencing data.

Homepage:

https://github.com/phac-nml/sequenoscope

License:

Apache-2.0

Recipe:

/sequenoscope/meta.yaml

package sequenoscope

versions:

0.0.5-1,  0.0.5-0

depends biopython:

>=1.7

depends fastp:

>=0.22.0,<=0.23.2

depends mash:

>=2.3

depends minimap2:

>=2.26

depends numpy:

depends pandas:

depends plotly:

>=5.16.1

depends pysam:

>=0.16.0

depends python:

>=3.7.12,<4

depends samtools:

>=1.6

depends scipy:

>=1.7.3

depends seqtk:

>=1.4

depends six:

>=1.14.0

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 sequenoscope

and update with::

   mamba update sequenoscope

To create a new environment, run:

mamba create --name myenvname sequenoscope

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/sequenoscope:<tag>

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

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