recipe phenix

Public Health England SNP calling pipeline







biotools: phenix

package phenix

(downloads) docker_phenix



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:


depends python_abi:

2.7.* *_cp27m

depends pyvcf:

depends pyyaml:

depends samtools:



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 phenix

and update with::

   mamba update phenix

To create a new environment, run:

mamba create --name myenvname phenix

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<tag>

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

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