Package Recipe 'capcruncher' — Bioconda documentation

recipe capcruncher

An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data.

Homepage:: sims-lab/CapCruncher
Documentation:: https://sims-lab.github.io/CapCruncher
License:: GPL3 / GPL-3.0-or-later
Recipe:: /capcruncher/meta.yaml
Links:: doi: 10.5281/zenodo.10629485

package capcruncher#

Versions:

0.3.14-1, 0.3.14-0, 0.3.12-0, 0.3.11-0, 0.3.10-0, 0.3.9-0, 0.3.8-0, 0.3.7-0, 0.3.6-0,

0.3.14-1, 0.3.14-0, 0.3.12-0, 0.3.11-0, 0.3.10-0, 0.3.9-0, 0.3.8-0, 0.3.7-0, 0.3.6-0, 0.3.5-0, 0.3.4-0, 0.2.3-0, 0.2.2-0, 0.1.1a1-0, 0.1.0a2-0

Depends:

on click <=8.2.0
on cookiecutter <=2.1.1
on cooler
on duckdb
on h5py
on loguru <=0.7.2
on more-itertools
on natsort
on numpy <=1.26.4
on pandas <=2.1.2
on plotly >5.0.0,<=5.10.0
on polars <=1.27.1
on protobuf <=6.30.2
on pulp <2.8.0
on pyarrow >11.0.0,<19.0.1
on pybedtools
on pyranges <=0.1.2
on pysam >0.15.0,<=0.21.0
on python >=3.10
on python-xxhash
on pyyaml >=6.0
on quarto
on ray
on seaborn-base
on sh
on snakemake-minimal <=7.32.4
on snakemake-wrapper-utils
on tqdm
on trackhub
on tracknado
on ujson
on xopen

Additional platforms:

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 capcruncher

to add into an existing workspace instead, run:

pixi add capcruncher

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 capcruncher

Alternatively, to install into a new environment, run:

conda create -n envname capcruncher

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/capcruncher:<tag>

(see capcruncher/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/capcruncher/README.html)