recipe masurca

MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.

Homepage:

https://masurca.blogspot.co.uk

Documentation:

https://github.com/alekseyzimin/masurca/blob/v4.1.2/README.md

Developer docs:

https://github.com/alekseyzimin/masurca

License:

GPL3 / GPL-3.0-only

Recipe:

/masurca/meta.yaml

Links:

biotools: masurca, doi: 10.1093/bioinformatics/btt476

package masurca

versions:

4.1.2-0,  4.1.1-2,  4.1.1-1,  4.1.1-0,  4.1.0-1,  4.1.0-0,  4.0.9-1,  4.0.9-0,  4.0.8-1, 

4.1.2-0,  4.1.1-2,  4.1.1-1,  4.1.1-0,  4.1.0-1,  4.1.0-0,  4.0.9-1,  4.0.9-0,  4.0.8-1,  4.0.8-0,  4.0.7-1,  4.0.7-0,  4.0.6-0,  3.4.2-1,  3.4.2-0,  3.4.1-0,  3.4.0-0,  3.3.9-0,  3.3.8-0,  3.3.7-0,  3.3.6-0,  3.3.5-0,  3.3.4-0,  3.3.3-0,  3.3.1-0,  3.3.0-0,  3.2.9-0,  3.2.8-0,  3.2.7-0

depends boost-cpp:

depends bwa:

depends bzip2:

>=1.0.8,<2.0a0

depends flye:

depends grep:

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends minimap2:

depends perl:

depends yaggo:

>=1.5.10,<1.6.0a0

requirements:

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 masurca

and update with::

   mamba update masurca

To create a new environment, run:

mamba create --name myenvname masurca

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/masurca:<tag>

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

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