:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'phenix' .. highlight: bash phenix ====== .. conda:recipe:: phenix :replaces_section_title: :noindex: Public Health England SNP calling pipeline :homepage: https://github.com/phe-bioinformatics/PHEnix :license: GPL3 :recipe: /`phenix `_/`meta.yaml `_ :links: biotools: :biotools:`phenix` .. conda:package:: phenix |downloads_phenix| |docker_phenix| :versions: ``1.4.1a-2``,  ``1.4.1a-1``,  ``1.4.1a-0`` :depends argparse: :depends bcftools: :depends bintrees: :depends biopython: :depends bowtie2: :depends bwa: :depends gatk: :depends matplotlib: :depends matplotlib-venn: :depends numpy: :depends picard: :depends psycopg2: :depends pysam: :depends python: ``>=2.7,<2.8.0a0`` :depends python_abi: ``2.7.* *_cp27m`` :depends pyvcf: :depends pyyaml: :depends samtools: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install phenix and update with:: conda update phenix or use the docker container:: docker pull quay.io/biocontainers/phenix: (see `phenix/tags`_ for valid values for ````) .. |downloads_phenix| image:: https://img.shields.io/conda/dn/bioconda/phenix.svg?style=flat :target: https://anaconda.org/bioconda/phenix :alt: (downloads) .. |docker_phenix| image:: https://quay.io/repository/biocontainers/phenix/status :target: https://quay.io/repository/biocontainers/phenix .. _`phenix/tags`: https://quay.io/repository/biocontainers/phenix?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/phenix/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/phenix/README.html