Package Recipe 'verkko'

recipe verkko

A hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate (HiFi, ONT Duplex, ONT HERRO) and long (ONT UL) reads.

Homepage:: https://github.com/marbl/verkko
Documentation:: https://github.com/marbl/verkko/blob/v2.3.2/README.md
License:: CC0
Recipe:: /verkko/meta.yaml
Links:: doi: 10.1038/s41587-023-01662-6, usegalaxy-eu: verkko

package verkko¶

Versions:

2.3.2-0, 2.3.1-0, 2.3-1, 2.3-0, 2.2.1-0, 2.2-0, 2.1-0, 2.0-0, 1.4.1-0,

2.3.2-0, 2.3.1-0, 2.3-1, 2.3-0, 2.2.1-0, 2.2-0, 2.1-0, 2.0-0, 1.4.1-0, 1.4-0, 1.3.1-0, 1.3-0, 1.2-0, 1.1-1, 1.1-0, 1.0-3, 1.0-2, 1.0-1, 1.0-0

Depends:

on _openmp_mutex >=4.5
on bamtools >=2.5
on bamtools >=2.5.3,<3.0a0
on biopython
on bwa >=0.7.17
on bzip2 >=1.0.8,<2.0a0
on findutils >=4.6.0
on graphaligner >=1.0.19
on gsl >=2.7,<2.8.0a0
on htslib >=1.23,<1.24.0a0
on libgcc >=14
on libgomp
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on mashmap >=3.0.6
on minimap2 >=2.28
on networkx >=2.6.3,<=3.5
on parasail-python >=1.3.3
on perl >=5.6
on pulp <=2.7.0
on pysam
on python >=3.9
on samtools >=1.17
on seqtk
on snakemake-minimal >=7.8.0,<8.0
on winnowmap >=2.0

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 verkko

to add into an existing workspace instead, run:

pixi add verkko

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 verkko

Alternatively, to install into a new environment, run:

conda create -n envname verkko

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/verkko:<tag>

(see verkko/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/verkko/README.html)