Installation¶

InStrain is written in python. There are a number of ways that it can be installed.

pip¶

To install inStrain using the PyPi python repository, simply run

$ pip install instrain

That’s it!

Pip is a great package with many options to change the installation parameters in various ways. For details, see pip documentation

bioconda¶

To inStrain inStrain from bioconda, run

$ conda install -c conda-forge -c bioconda -c defaults instrain

From source¶

To install inStrain from the source code, run

$ git clone https://github.com/MrOlm/instrain.git

$ cd instrain

$ pip install .

Dependencies¶

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

Essential

samtools This is needed for pysam

Optional

coverM This is needed for the quick_profile operation
Prodigal This is needed to profile on a gene by gene level

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.

Docker image¶

A Docker image with inStrain and dependencies already installed is available on Docker Hub at mattolm/instrain. This image also has a wrapper script in it to make it easier to use inStrain with AWS. See the docker folder of the GitHub page for use instructions.