recipe smartmap

SmartMap: Bayesian Analysis of Ambiguously Mapped Reads






package smartmap

(downloads) docker_smartmap



depends bedtools:

depends bowtie2:

depends hisat2:

depends libgcc-ng:


depends libstdcxx-ng:


depends libzlib:


depends python:


depends samtools:




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 smartmap

and update with::

   mamba update smartmap

To create a new environment, run:

mamba create --name myenvname smartmap

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<tag>

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

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