Package Recipe 'clever-toolkit'

recipe clever-toolkit

The CLEVER Toolkit.

Homepage:: https://bitbucket.org/tobiasmarschall/clever-toolkit
Documentation:: https://bitbucket.org/tobiasmarschall/clever-toolkit/wiki/Home
License:: GPL3 / GPL-3.0-only
Recipe:: /clever-toolkit/meta.yaml

CTK is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads.

package clever-toolkit¶

Versions:

2.4-14, 2.4-13, 2.4-12, 2.4-11, 2.4-10, 2.4-9, 2.4-8, 2.4-7, 2.4-6,

2.4-14, 2.4-13, 2.4-12, 2.4-11, 2.4-10, 2.4-9, 2.4-8, 2.4-7, 2.4-6, 2.4-5, 2.4-0, 2.3-0, 2.2.1-0, 2.1-3, 2.0rc4-3, 2.0rc4-2, 2.0rc3-1, 2.0rc3-0

Depends:

on bedtools
on bwa
on libgcc >=13
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on matplotlib-base
on python 3.*
on samtools

Additional platforms:

linux-aarch64, osx-arm64

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 clever-toolkit

to add into an existing workspace instead, run:

pixi add clever-toolkit

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 clever-toolkit

Alternatively, to install into a new environment, run:

conda create -n envname clever-toolkit

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/clever-toolkit:<tag>

(see clever-toolkit/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/clever-toolkit/README.html)