recipe novobreak

local assembly for breakpoint detection in cancer genomes

Homepage:

https://github.com/czc/nb_distribution

License:

MIT

Recipe:

/novobreak/meta.yaml

package novobreak

versions:

1.1.3rc-10,  1.1.3rc-9,  1.1.3rc-8,  1.1.3rc-7,  1.1.3rc-6,  1.1.3rc-5,  1.1.3rc-4,  1.1.3rc-3,  1.1.3rc-2, 

1.1.3rc-10,  1.1.3rc-9,  1.1.3rc-8,  1.1.3rc-7,  1.1.3rc-6,  1.1.3rc-5,  1.1.3rc-4,  1.1.3rc-3,  1.1.3rc-2,  1.1.3rc-1,  1.1.3rc-0

depends bwa:

>=0.7.10

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends perl:

depends samtools:

1.*

depends ssake:

depends zlib:

requirements:

additional platforms:

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 novobreak

and update with::

   mamba update novobreak

To create a new environment, run:

mamba create --name myenvname novobreak

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/novobreak:<tag>

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

Notes

This package makes novobreak available via a wrapper in PATH, called `run_novobreak`, which takes all arguments of the run_novoBreak.sh script except the first, which is automatically inferred.

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