recipe haploconduct

HaploConduct is a package designed for reconstruction of individual haplotypes from next generation sequencing data, in particular Illumina. It provides two methods, SAVAGE and POLYTE, which can be run through the haploconduct wrapper.






package haploconduct

(downloads) docker_haploconduct



depends boost-cpp:


depends bwa:

depends kallisto:


depends libgcc-ng:


depends libstdcxx-ng:


depends python:


depends python_abi:

2.7.* *_cp27mu

depends rust-overlaps:

depends samtools:


depends scipy:



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 haploconduct

and update with::

   mamba update haploconduct

To create a new environment, run:

mamba create --name myenvname haploconduct

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

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