recipe sam2lca

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

Homepage:

https://github.com/maxibor/sam2lca

License:

GPL-3.0

Recipe:

/sam2lca/meta.yaml

package sam2lca

versions:

1.1.4-0,  1.1.3-0,  1.1.2-1,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.0-1,  1.0.0-0

depends click:

depends numpy:

depends pandas:

depends pysam:

depends python:

>=3.7

depends python-rocksdb:

depends scipy:

depends taxopy:

>=0.10.2

depends tqdm:

depends xopen:

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 sam2lca

and update with::

   mamba update sam2lca

To create a new environment, run:

mamba create --name myenvname sam2lca

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/sam2lca:<tag>

(see `sam2lca/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an badge with the following MarkDown:

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