Installation
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
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.