Package Recipe 'meraculous'

recipe meraculous

Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.

Homepage:: https://jgi.doe.gov/data-and-tools/meraculous/
License:: GPLv3
Recipe:: /meraculous/meta.yaml
Links:: doi: 10.1371/journal.pone.0023501

package meraculous¶

Versions:

2.2.6-9, 2.2.6-8, 2.2.6-7, 2.2.6-6, 2.2.6-5, 2.2.6-4, 2.2.6-3, 2.2.6-2, 2.2.6-1,

2.2.6-9, 2.2.6-8, 2.2.6-7, 2.2.6-6, 2.2.6-5, 2.2.6-4, 2.2.6-3, 2.2.6-2, 2.2.6-1, 2.2.6-0, 2.2.5.1.1.ga103cd6-0, 2.2.5-0, 2.2.4-1, 2.2.4-0

Depends:

on boost-cpp
on gnuplot >=3.7
on libgcc >=13
on libgd >=2.0
on libgd >=2.3.3,<2.4.0a0
on libstdcxx >=13
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-log-log4perl >=1.31

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 meraculous

to add into an existing workspace instead, run:

pixi add meraculous

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 meraculous

Alternatively, to install into a new environment, run:

conda create -n envname meraculous

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/meraculous:<tag>

(see meraculous/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/meraculous/README.html)