recipe harpy

Process raw haplotagging data, from raw sequences to phased haplotypes.



Developer docs:





package harpy

(downloads) docker_harpy



depends bcftools:

depends bioconductor-complexheatmap:

depends bwa:

depends fastp:

depends fastqc:

depends hapcut2:

depends icu:

depends leviathan:

depends libzlib:

depends llvm-openmp:

depends multiqc:

depends naibr-plus:

depends pysam:

depends python:


depends python_abi:

3.9.* *_cp39

depends r-base:

depends r-circlize:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-ggridges:

depends r-knitr:

depends r-magrittr:

depends r-plotly:

depends r-rmarkdown:

depends r-stitch:

depends r-tidyr:

depends r-viridislite:

depends rich-click:

depends sambamba:

depends samtools:

depends seqtk:

depends snakemake:


depends tabix:

depends xz:



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 harpy

and update with::

   mamba update harpy

To create a new environment, run:

mamba create --name myenvname harpy

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 `harpy/tags`_ for valid values for ``<tag>``)

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