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 boost-cpp:

depends gnuplot:

>=3.7

depends libgcc:

>=13

depends libgd:

>=2.0

depends libgd:

>=2.3.3,<2.4.0a0

depends libstdcxx:

>=13

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-log-log4perl:

>=1.31

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install meraculous

and update with::

   mamba update meraculous

To create a new environment, run:

mamba create --name myenvname meraculous

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `meraculous/tags`_ for valid values for ``<tag>``)

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