:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'seq-seq-pan' .. highlight: bash seq-seq-pan =========== .. conda:recipe:: seq-seq-pan :replaces_section_title: :noindex: seq\-seq\-pan :homepage: https://gitlab.com/chrjan/seq-seq-pan :license: FreeBSD :recipe: /`seq-seq-pan `_/`meta.yaml `_ seq\-seq\-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN\-genome data structure and a whole\-genome\-alignment. .. conda:package:: seq-seq-pan |downloads_seq-seq-pan| |docker_seq-seq-pan| :versions: .. raw:: html
1.1.0-11.1.0-01.0.1-41.0.1-31.0.1-11.0.1-01.0.0-41.0.0-31.0.0-1 ``1.1.0-1``,  ``1.1.0-0``,  ``1.0.1-4``,  ``1.0.1-3``,  ``1.0.1-1``,  ``1.0.1-0``,  ``1.0.0-4``,  ``1.0.0-3``,  ``1.0.0-1``,  ``1.0.0-0`` .. raw:: html
:depends biopython: ``1.69`` :depends blat: ``35`` :depends libgenome: ``1.3.1 hc9558a2_2`` :depends mauvealigner: ``1.2.0`` :depends openjdk: :depends python: ``>=3`` :depends snakemake: :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 seq-seq-pan and update with:: mamba update seq-seq-pan To create a new environment, run:: mamba create --name myenvname seq-seq-pan 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/seq-seq-pan: (see `seq-seq-pan/tags`_ for valid values for ````) .. |downloads_seq-seq-pan| image:: https://img.shields.io/conda/dn/bioconda/seq-seq-pan.svg?style=flat :target: https://anaconda.org/bioconda/seq-seq-pan :alt: (downloads) .. |docker_seq-seq-pan| image:: https://quay.io/repository/biocontainers/seq-seq-pan/status :target: https://quay.io/repository/biocontainers/seq-seq-pan .. _`seq-seq-pan/tags`: https://quay.io/repository/biocontainers/seq-seq-pan?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/seq-seq-pan/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/seq-seq-pan/README.html