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Installation

pip (simple install)

If you already have annotated vcf files and you do not need to do any variant calling or annotation, you can simply install the basic tbtAMR python package. Just to be clear this is a bare bones installation and you will not be able to use fastq files or unannotated vcf files as inputs.. If you require annotation - please see below.

You will need have python=3.10 or greater installed on your system (although management with mamba or conda is also ofcourse possible - actually recommended)

Optional: 

mamba create -n tbtamr python=3.10
mamba activate tbtamr
OR 
conda create -n tbtamr python=3.10
conda activate tbtamr
Required: 
pip3 install tbtamr

You can use conda to install the full tbtAMR package. This installation allows you to generate a vcf file from paired end reads, annotate a vcf file and/or generate genomic DST results.

conda (or mamba) create -n tbtamr tbtamr
conda activate tbtamr 
tbtamr -v
> 1.0.3

Custom

tbtAMR + annotation

In some cases you may have a vcf file - but need annotation (and do not want any of the variant calling dependencies). 

conda(mamba) create -n tbtamr snpEff
conda(mamba) activate tbtamr
pip3 install tbtamr==1.0.3

tbtamr + lineage calling

If you would like to run lineage calling you can install pathogenprofiler into your environment - note that this requires bcftools.

conda activate tbtamr
conda install bcftools (if you use conda to install tbtamr there is NO NEED for this step - only install bcftools if you use the pip3 simple install approach)
pip3 install git+https://github.com/jodyphelan/pathogen-profiler@v4.3.0
pip3 install pysam joblib tqdm pydantic requests

I have not suggested to install this with conda (which it absolutely can be if that works for you) as some of the dependency versions may clash with the mutAMR compatible dependencies. If you wish to use conda to install pathogen-profiler please be aware that there may be unexpected behaviour