recipe canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.

Homepage:

https://github.com/marbl/canu

Documentation:

https://canu.readthedocs.org

License:

GPL / GPL-2.0-or-later and others

Recipe:

/canu/meta.yaml

Links:

usegalaxy-eu: canu, biotools: canu, biotools: hicanu, doi: 10.1101/gr.215087.116, doi: 10.1038/nbt.4277, doi: 10.1101/gr.263566.120

package canu

versions:

2.3-0,  2.2-0,  2.1.1-2,  2.1.1-1,  2.1.1-0,  2.0-0,  1.9-1,  1.9-0,  1.8-2, 

2.3-0,  2.2-0,  2.1.1-2,  2.1.1-1,  2.1.1-0,  2.0-0,  1.9-1,  1.9-0,  1.8-2,  1.8-1,  1.8-0,  1.7.1-0,  1.7-0,  1.6-1,  1.5-1,  1.5-0,  1.4-2,  1.4-1,  1.4-0,  1.3-0,  1.1-0

depends _openmp_mutex:

>=4.5

depends boost-cpp:

depends gnuplot:

>=5.2

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends minimap2:

depends openjdk:

>=20

depends perl:

depends perl-filesys-df:

depends samtools:

depends xorg-libxfixes:

>=6.0.1,<7.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 canu

and update with::

   mamba update canu

To create a new environment, run:

mamba create --name myenvname canu

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/canu:<tag>

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

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