recipe jcvi

Python utility libraries on genome assembly, annotation, and comparative genomics.

Homepage:

https://github.com/tanghaibao/jcvi

Documentation:

https://github.com/tanghaibao/jcvi/wiki

License:

BSD / BSD-2-Clause

Recipe:

/jcvi/meta.yaml

Links:

doi: 10.1002/imt2.211

JCVI utility libraries

package jcvi

versions:

1.5.4-0,  1.4.16-0,  1.4.15-1,  1.4.15-0,  1.4.11-0,  1.4.10-0,  1.4.9-0,  1.3.9-1,  1.3.9-0, 

1.5.4-0,  1.4.16-0,  1.4.15-1,  1.4.15-0,  1.4.11-0,  1.4.10-0,  1.4.9-0,  1.3.9-1,  1.3.9-0,  1.3.8-0,  1.3.6-0,  1.3.5-1,  1.3.4-1,  1.3.4-0,  1.2.7-3,  1.2.7-1,  1.2.7-0,  1.2.6-0,  1.2.5-0,  1.2.4-0,  1.2.3-0,  1.1.19-1,  1.1.19-0,  1.1.18-0,  1.1.17-2,  1.1.17-1,  1.1.17-0,  1.1.16-0,  1.1.15-0,  1.1.14-0,  1.1.12-0,  1.1.11-1,  1.1.11-0,  1.1.10-1,  1.1.10-0,  1.1.8-0,  1.1.5-0,  1.0.14-0,  1.0.13-0,  1.0.12-0,  1.0.11-0,  1.0.10-0,  1.0.9-1,  1.0.9-0,  1.0.8-1,  1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  0.9.14-0,  0.9.13-0,  0.9.12-0,  0.9.11-0,  0.9.10-0,  0.9.9-0,  0.9.6-0,  0.8.12-1,  0.8.12-0,  0.8.4-1,  0.8.4-0

depends biopython:

depends boto3:

depends brewer2mpl:

depends crossmap:

depends deap:

depends ete3:

depends ftpretty:

depends gffutils:

depends goatools:

depends imagemagick:

depends jinja2:

depends last:

depends libgcc:

>=13

depends libmagic:

depends matplotlib-base:

depends more-itertools:

depends natsort:

depends networkx:

depends numpy:

>=1.22.4,<2.0a0

depends pybedtools:

depends pyefd:

depends pypdf:

depends pytesseract:

depends python:

>=3.10,<3.11.0a0

depends python-graphviz:

depends python_abi:

3.10.* *_cp310

depends r-ggplot2:

depends r-tinytex:

depends rich:

depends scikit-image:

depends scipy:

depends seaborn-base:

depends ucsc-liftover:

depends wand:

depends webcolors:

requirements:

additional platforms:

linux-aarch64

Installation

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 quay.io/biocontainers/jcvi:<tag>

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

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