:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'samestr' .. highlight: bash samestr ======= .. conda:recipe:: samestr :replaces_section_title: :noindex: 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: :doi:`10.1186/s40168-022-01251-w` .. conda:package:: samestr |downloads_samestr| |docker_samestr| :versions: ``1.2024.2.post1-0``,  ``1.2023.4-0``,  ``1.2023.3-0`` :depends biopython: ``1.81`` :depends blast: ``>=2.6.0`` :depends mafft: ``7.515`` :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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `samestr/tags`_ for valid values for ````) .. |downloads_samestr| image:: https://img.shields.io/conda/dn/bioconda/samestr.svg?style=flat :target: https://anaconda.org/bioconda/samestr :alt: (downloads) .. |docker_samestr| image:: https://quay.io/repository/biocontainers/samestr/status :target: https://quay.io/repository/biocontainers/samestr .. _`samestr/tags`: https://quay.io/repository/biocontainers/samestr?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/samestr/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/samestr/README.html