Package Recipe 'jcvi'

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:

1.6.4-1, 1.6.4-0, 1.6.3-1, 1.6.3-0, 1.6.1-1, 1.6.1-0, 1.5.11-1, 1.5.11-0, 1.5.10-0,

1.6.4-1, 1.6.4-0, 1.6.3-1, 1.6.3-0, 1.6.1-1, 1.6.1-0, 1.5.11-1, 1.5.11-0, 1.5.10-0, 1.5.9-0, 1.5.8-0, 1.5.7-0, 1.5.6-0, 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:

on biopython
on boto3
on crossmap
on deap
on ete3
on ftpretty
on gffutils
on goatools
on imagemagick
on jinja2
on last
on libgcc >=14
on libmagic
on matplotlib-base
on more-itertools
on natsort
on networkx
on numpy >=1.21,<3
on palettable
on pybedtools
on pyefd
on pypdf
on pytesseract
on python >=3.10,<3.11.0a0
on python-graphviz
on python_abi 3.10.* *_cp310
on r-ggplot2
on r-tinytex
on rich
on scikit-image
on scipy
on seaborn-base
on ucsc-liftover
on wand
on webcolors

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install jcvi

to add into an existing workspace instead, run:

pixi add jcvi

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install jcvi

Alternatively, to install into a new environment, run:

conda create -n envname jcvi

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/jcvi:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html)