recipe geno2phenotb

Prediction of Mycobacterium tuberculosis drug resistance from WGS data

Homepage:

https://github.com/msmdev/geno2phenoTB

Documentation:

https://geno2phenotb.readthedocs.io/en/latest

License:

LGPL-3.0-only

Recipe:

/geno2phenotb/meta.yaml

geno2phenoTB is a machine learning based tool to predict resistance of Mycobacterium tuberculosis against antibiotics using whole-genome sequencing data.

package geno2phenotb

(downloads) docker_geno2phenotb

versions:

1.0.1-0,  1.0.0-0

depends bwa:

0.7.17.*

depends gatk:

3.8.*

depends imbalanced-learn:

0.8.1.*

depends importlib_metadata:

depends joblib:

1.2.*

depends mtbseq:

1.0.4.*

depends numpy:

1.21.5.*

depends packaging:

21.*

depends pandas:

0.25.3.*

depends perl-base:

2.23.*

depends python:

3.8.17.*

depends requests:

2.*

depends samtools:

1.6.*

depends scikit-learn:

0.24.2.*

depends scipy:

1.7.3.*

depends setuptools:

depends tqdm:

4.*

depends wheel:

0.37.*

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 geno2phenotb

and update with::

   mamba update geno2phenotb

To create a new environment, run:

mamba create --name myenvname geno2phenotb

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/geno2phenotb:<tag>

(see `geno2phenotb/tags`_ for valid values for ``<tag>``)

Download stats

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/geno2phenotb/README.html)