recipe cgat-apps

Computational Genomics Analysis Toolkit






package cgat-apps

(downloads) docker_cgat-apps



depends alignlib-lite:

depends bedtools:

depends biopython:

depends cgatcore:

depends coreutils:

depends grep:

depends htslib:


depends libgcc-ng:


depends libstdcxx-ng:


depends matplotlib-base:

depends numpy:


depends pandas:

depends pybedtools:

depends pybigwig:

depends pysam:


depends python:


depends python_abi:

3.10.* *_cp310

depends pyyaml:

depends quicksect:

depends scikit-learn:

depends scipy:

depends sortedcontainers:

depends ucsc-bedgraphtobigwig:

depends ucsc-wigtobigwig:

depends zlib:



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 cgat-apps

and update with::

   mamba update cgat-apps

To create a new environment, run:

mamba create --name myenvname cgat-apps

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 `cgat-apps/tags`_ for valid values for ``<tag>``)

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