recipe galru

Rapid spoligotyping for Mycobacterium tuberculosis directly from long read sequencing






package galru

(downloads) docker_galru



depends bedtools:

depends biopython:


depends blast:

depends cd-hit:

depends minced:

depends minimap2:

depends mlst:

depends ncbi-genome-download:

depends pyfastaq:


depends python:


depends pyyaml:

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 galru

and update with::

   mamba update galru

To create a new environment, run:

mamba create --name myenvname galru

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

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