:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'panpasco' .. highlight: bash panpasco ======== .. conda:recipe:: panpasco :replaces_section_title: :noindex: Pipeline for pangenome mapping and pairwise SNP distance :homepage: https://gitlab.com/rki_bioinformatics/panpasco :license: MIT :recipe: /`panpasco `_/`meta.yaml `_ PANPASCO uses linear computational pan\-genomes and pairwise SNP distance calculation to improve distance matrix analyses .. conda:package:: panpasco |downloads_panpasco| |docker_panpasco| :versions: ``1.0.1-0``,  ``1.0.0-0`` :depends bedtools: ``2.27.*`` :depends bioconductor-genomicranges: :depends bwa: ``0.7.17.*`` :depends flash: ``1.2.11.*`` :depends gatk: ``3.8.*`` :depends picard: ``2.18.*`` :depends python: ``>3`` :depends r-argparse: :depends r-base: ``>=4.0,<4.1.0a0`` :depends samtools: :depends seqtk: :depends snakemake: :depends tabix: :depends trimmomatic: ``0.36.*`` :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 panpasco and update with:: mamba update panpasco To create a new environment, run:: mamba create --name myenvname panpasco 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/panpasco: (see `panpasco/tags`_ for valid values for ````) .. |downloads_panpasco| image:: https://img.shields.io/conda/dn/bioconda/panpasco.svg?style=flat :target: https://anaconda.org/bioconda/panpasco :alt: (downloads) .. |docker_panpasco| image:: https://quay.io/repository/biocontainers/panpasco/status :target: https://quay.io/repository/biocontainers/panpasco .. _`panpasco/tags`: https://quay.io/repository/biocontainers/panpasco?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/panpasco/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/panpasco/README.html