Install

TB-Profiler can be installed using a variety of different methods. The easiest is to use conda but you can also install manually.

Conda

Conda can function as a package manages are is available here. If you have conda make sure the bioconda and conda-forge channels are added:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then you can install with:

conda install -c bioconda tb-profiler

If this is taking a long time or complains about inconsistencies there are a few things we can do. The first is switching to mamba install. mamba basically is a drop-in replacement for conda, but is a lot faster. If you don't have it yet, you can install with:

conda install -c conda-forge mamba

Second, tb-profiler comes bundled with a lot of software. This often can cause compatibility issues with other software installed in your conda base environemnt. It is therefor recommended to intall tb-profiler in its own enviroment with:

mamba create -n tb-profiler tb-profiler

Manually

It is possible to install manually. The following pre-requisites will be needed at runtime: trimmomatic (>=v0.38), bwa (>=v0.7.17), minimap2 (>=v2.16), bowtie2 (>=v2.3.5), samtools (>=v1.9), bcftools (>=v1.9), GATK (>=v4.1.4.0), tqdm (>=v4.32.2) and parallel (>=v20190522). The pipeline should work and has been tested on the program versions indicated in parentheses.

To install the library, you can then use:

pip3 install git+https://github.com/jodyphelan/TBProfiler.git
pip3 install git+https://github.com/jodyphelan/pathogen-profiler.git
mkdir `python -c "import sys; print(getattr(sys, 'base_prefix', getattr(sys, 'real_prefix', sys.prefix)));"`
tb-profiler update_tbdb

Docker

The pipline can also be run through docker. This is handy when the above methods fail for whatever reason. Pull the latest image using:

docker pull quay.io/biocontainers/tb-profiler:4.3.0--pypyh5e36f6f_0

If the above method don't work please feel free to raise an issue. We'll try help you get up and running!