recipe sam2pairwise

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read

Homepage:

https://github.com/mlafave/sam2pairwise

Documentation:

https://github.com/mlafave/sam2pairwise/blob/master/README.md

License:

MIT

Recipe:

/sam2pairwise/meta.yaml

package sam2pairwise

(downloads) docker_sam2pairwise

versions:

1.0.0-0

depends libgcc:

>=12

depends libstdcxx:

>=12

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 sam2pairwise

and update with::

   mamba update sam2pairwise

To create a new environment, run:

mamba create --name myenvname sam2pairwise

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/sam2pairwise:<tag>

(see `sam2pairwise/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sam2pairwise/README.html)