recipe hamip

HaMiP is A scalable, accurate, and efficient solution for hydroxymethylation analysis of CMS-IP data.



MIT / License :: OSI Approved :: MIT



package hamip

(downloads) docker_hamip


depends bedtools:

depends bioconductor-deseq2:

depends bioconductor-genefilter:

depends gawk:

depends matplotlib-base:

depends moabs:

depends pandas:

depends python:


depends pyyaml:

depends r-base:


depends r-desctools:

depends ucsc-fetchchromsizes:



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 hamip

and update with::

   mamba update hamip

To create a new environment, run:

mamba create --name myenvname hamip

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

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