recipe strainy

assembly-based metagenomic strain phasing using long reads

Homepage:

https://github.com/katerinakazantseva/strainy

License:

GPL3 / GPL-3.0-or-later

Recipe:

/strainy/meta.yaml

package strainy

versions:

1.1-1,  1.1-0

depends bcftools:

>=1.14

depends biopython:

depends flye:

depends gfapy:

depends karateclub:

depends matplotlib-base:

depends minimap2:

depends networkx:

>=2.6,<3.4

depends numpy:

>=1.24,<1.27

depends pandas:

>=1.3,<3

depends pygraphviz:

depends pysam:

>=0.20,<0.23

depends python:

>=3.8

depends python-edlib:

depends samtools:

>=1.14

depends scipy:

>=1.8,<1.13

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 strainy

and update with::

   mamba update strainy

To create a new environment, run:

mamba create --name myenvname strainy

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/strainy:<tag>

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

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