SPR detailed installation instructions

systemPipeR Installation

To install the systemPipeR package (H Backman and Girke 2016), please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

To obtain the most recent updates immediately, one can install it directly from github as follow:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("tgirke/systemPipeR", build_vignettes = TRUE, 
    dependencies = TRUE)

Third-party software tools in SPR

This guide provides detailed installation instructions for the software tools used within systemPipeR package. This guide provides the instruction for a Linux system.


Burrow-Wheeler Aligner (BWA) for short-read alignment (Li 2013).

git clone https://github.com/lh3/bwa.git
cd bwa
vim ~/.bashrc ## Open the Bash shell script 
export PATH=$PATH:/path/to/bwa ## "/path/to/bwa" is an example! Replace with real PATH
source ~/.bashrc
bwa ## Test if the installation was successful

Note: In some systems, ~/.bash_profile is used in place of ~/.bashrc.

More information about how to set an enviroment variable here.


Please check the BLAST Command Line Applications User Manual to find the installation introduction for your system environment.

Download the latest version from here, as the following example:

wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.11.0+-x64-linux.tar.gz
tar zxvpf ncbi-blast-2.11.0+-x64-linux.tar.gz ncbi-blast-2.11.0+/
cd ncbi-blast-2.11.0+/
export PATH=$PATH:/path/to//ncbi-blast-2.11.0+/bin ## "/path/to/ncbi-blast-2.11.0+" is an example! Replace with real PATH



H Backman, Tyler W, and Thomas Girke. 2016. “systemPipeR: NGS workflow and report generation environment.” BMC Bioinformatics 17 (1): 388. https://doi.org/10.1186/s12859-016-1241-0.

Li, Heng. 2013. “Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM,” March. http://arxiv.org/abs/1303.3997.