recipe savage

SAVAGE (Strain Aware VirAl GEnome assembly) reconstructs individual (viral) haplotypes from a mixed sample.

Homepage:

https://github.com/HaploConduct/HaploConduct/tree/master/savage

License:

GPL v3

Recipe:

/savage/meta.yaml

package savage

versions:

0.4.2-2,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-2,  0.4.0-1,  0.4.0-0,  0.3.0-0,  0.2.1-1, 

0.4.2-2,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-2,  0.4.0-1,  0.4.0-0,  0.3.0-0,  0.2.1-1,  0.2.1-0

depends _openmp_mutex:

>=4.5

depends boost-cpp:

>=1.74.0,<1.74.1.0a0

depends bwa:

depends kallisto:

>=0.43.0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends rust-overlaps:

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 savage

and update with::

   mamba update savage

To create a new environment, run:

mamba create --name myenvname savage

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/savage:<tag>

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

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