recipe samestr

SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.

Homepage:

https://github.com/danielpodlesny/samestr/

Developer docs:

https://github.com/danielpodlesny/samestr

License:

AGPL / AGPL-3.0-or-later

Recipe:

/samestr/meta.yaml

Links:

doi: 10.1186/s40168-022-01251-w

package samestr

versions:

1.2024.8-0,  1.2024.2.post1-0,  1.2023.4-0,  1.2023.3-0

depends biopython:

1.81

depends blast:

>=2.6.0

depends mafft:

7.525

depends muscle:

3.8.1551

depends numpy:

1.24.2

depends pandas:

1.5.3

depends pysam:

0.20.0

depends python:

>=3.9

depends samtools:

0.1.19

depends scipy:

1.10.0

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 samestr

and update with::

   mamba update samestr

To create a new environment, run:

mamba create --name myenvname samestr

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/samestr:<tag>

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

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