recipe tbtamr

A tool implementing TB-Profiler for reporting of genomic DST for M. tuberculosis in a CPHL

Homepage:

https://github.com/MDU-PHL/tbtamr

License:

GPL3 / GPL-3.0-or-later

Recipe:

/tbtamr/meta.yaml

package tbtamr

versions:

0.0.4-1,  0.0.4-0

depends bcftools:

depends bedtools:

depends bwa:

depends csvtk:

depends delly:

depends freebayes:

depends pandas:

depends psutil:

depends python:

>=3.8

depends requests:

depends samclip:

depends samtools:

1.12.*

depends snpeff:

5.0.*

depends tqdm:

depends xlsxwriter:

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 tbtamr

and update with::

   mamba update tbtamr

To create a new environment, run:

mamba create --name myenvname tbtamr

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/tbtamr:<tag>

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

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Link to this page

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