InStrain is written in python. There are a number of ways that it can be installed.
To install inStrain using the PyPi python repository, simply run
$ pip install instrain
Pip is a great package with many options to change the installation parameters in various ways. For details, see pip documentation
To inStrain inStrain from bioconda, run
$ conda install -c conda-forge -c bioconda -c defaults instrain
To install inStrain from the source code, run
$ git clone https://github.com/MrOlm/instrain.git $ cd instrain $ pip install .
inStrain requires a few other programs to run. Not all dependencies are needed for all operations. There are a number of python package dependencies, but those should install automatically when inStrain is installed using pip
- samtools This is needed for pysam
Pre-built genome database¶
An established set of public genomes can be downloaded for your inStrain analysis at the following link - https://doi.org/10.5281/zenodo.4441269. See Tutorial #2 in Tutorial for usage instructions.