Installation

Recommended installation

SISTEM can be easily installed with conda from the bioconda channel. If you have not used bioconda before, run the one-time setup command:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

For best practices, install SISTEM into a new environment. You can do so as follows:

conda create -n SISTEM
conda activate SISTEM
conda install -c bioconda sistem

Make sure to activate the SISTEM environment before every use.

Note: If installing using conda, you may experience difficulties installing a dependency package named dwgsim, particularly on OSX machines. You can install SISTEM without dwgsim for Python version >=3.9 using pip:

pip install sistem

The dwgsim package is used to generate synthetic sequencing reads, and is only necessary if that is the intended use of SISTEM. For all other applications, installing SISTEM with pip as-is will be sufficient. If users experience difficulties installing with conda but intend to generate sequencing reads, you can first install SISTEM using pip and then install a binary for dwgsim manually from here. You will also need an executable for samtools. Please see additional details on installing these two dependencies in the following section.

Manual installation

Users can install SISTEM manually by downloading the source code and setting up an environment with all the necessary packages. The remainder of this section provides instructions on how to install SISTEM this way.

You can download the source code by cloning this repository:

git clone https://github.com/samsonweiner/sistem.git

SISTEM depends on the following Python packages, which can be installed with package managers like pip or conda.

• Numpy

• Scipy

• scikit-learn

• msprime

• Biopython

• Pyfaidx

• setuptools

Once installed, cd into the SISTEM repository and install the project:

pip install .

If generating synthetic sequencing reads, SISTEM also requires that the following external packages be installed and configured on the environment.

• samtools

• dwgsim version >=0.1.13

You can also install the packages individually by following the instructions found on the package homepage. If this option is used, the downloaded binaries must be compiled and the directories containing each binary must be added to your $PATH variable. For example,

export PATH=/path/to/bin:$PATH

You may also wish to add this line to your ~/.bashrc or /.bash_profile configuration file to avoid having to retype this command on login.