recipe jcvi

Python utility libraries on genome assembly, annotation and comparative genomics



BSD / BSD-2-Clause



JCVI utility libraries

package jcvi

(downloads) docker_jcvi



depends biopython:

depends boto3:

depends brewer2mpl:

depends coveralls:

depends deap:

depends ete3:

depends gffutils:

depends goatools:

depends graphviz:

depends jinja2:

depends last:

depends libgcc-ng:


depends matplotlib-base:

depends more-itertools:

depends natsort:

depends networkx:

depends numpy:


depends pypdf2:

depends python:


depends python_abi:

3.10.* *_cp310

depends pyyaml:

depends r-ggplot2:

depends r-tinytex:

depends rich:

depends scipy:

depends seaborn-base:

depends ucsc-liftover:



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 jcvi

and update with::

   mamba update jcvi

To create a new environment, run:

mamba create --name myenvname jcvi

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

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