recipe intemap

Integrated metagenomic assembly pipeline for short reads





package intemap

(downloads) docker_intemap



depends abyss:

depends bowtie2:

depends idba:

depends jellyfish:

depends libgcc:

depends mummer:

depends python:


depends quake:

depends wgs-assembler:



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 intemap

and update with::

   mamba update intemap

To create a new environment, run:

mamba create --name myenvname intemap

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 `intemap/tags`_ for valid values for ``<tag>``)

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