Pre-requisite for installing SyRI

C/C++ compiler

g++

Python

SyRI needs Python3.5 and depends on the following python libraries: Cython, Numpy, Scipy, Pandas, Igraph, Biopython, psutil, pysam

All these packages are available through anaconda and can be installed using:

conda install cython numpy scipy pandas=0.23.4 biopython psutil matplotlib=3.0.0
conda install -c conda-forge python-igraph
conda install -c bioconda pysam

# Additionally, if using chroder
conda install -c bioconda longestrunsubsequence 

Whole genome aligner

SyRI uses whole genome alignments as input. Users can use any aligner of their choice. SyRI accepts alignment input in SAM/BAM format or in a tab-separated value format with CIGAR string information for each alignment. If the user wants to use MUMmer, then .delta file can be used in place of CIGAR strings. See fileformat for more information.

Installation guide

Download (or clone) the repository for SyRI
Open the directory where setup.py is (we will call it as cwd) and in the terminal run:

python3 setup.py install		            # Install syri
chmod +x syri/bin/syri syri/bin/chroder	syri/bin/plotsr	# Make files executable

All executables would be in cwd/syri/bin/.