Package Recipe 'troika-tb'

recipe troika-tb

A pipeline implementing TB-Profiler for batch detection and reporting of anti-microbial resistance in TB for public health and clinical use.

Homepage:: https://github.com/kristyhoran/troika
License:: GPL-3.0
Recipe:: /troika-tb/meta.yaml

package troika-tb¶

Versions:

0.0.5-0

Depends:

on amply
on appdirs
on biopython >=1.70
on chardet
on configargparse
on docutils
on jinja2
on markupsafe
on nbformat
on numpy
on packaging
on pandas >=1.1.4
on pluggy >=0.13.1
on psutil
on pyparsing >=2.4.7
on pytest
on python >=3.7
on pyyaml
on requests
on setuptools-scm
on sh
on six
on snakemake >=5.9.1
on svgwrite
on toml
on urllib3
on xlsxwriter

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install troika-tb

to add into an existing workspace instead, run:

pixi add troika-tb

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install troika-tb

Alternatively, to install into a new environment, run:

conda create -n envname troika-tb

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/troika-tb:<tag>

(see troika-tb/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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/troika-tb/README.html)