recipe cuttlefish

Construction of the compacted de Bruijn graph efficiently

Homepage:

https://github.com/COMBINE-lab/cuttlefish

Documentation:

https://github.com/COMBINE-lab/cuttlefish#readme

License:

BSD-3-Clause

Recipe:

/cuttlefish/meta.yaml

Links:

doi: 10.1093/bioinformatics/btab309, doi: 10.1186/s13059-022-02743-6

package cuttlefish

versions:

2.2.0-2,  2.2.0-1,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.0-1,  2.0.0-0,  1.0.0-1,  1.0.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=12

depends libjemalloc:

>=5.3.0

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends zlib:

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 cuttlefish

and update with::

   mamba update cuttlefish

To create a new environment, run:

mamba create --name myenvname cuttlefish

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/cuttlefish:<tag>

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

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