README

VISPA2: A Scalable Pipeline for High-Throughput Identification and Annotation of Vector Integration Sites.

Authors: Giulio Spinozzi, Andrea Calabria.

Online web site for demo purpose: http://openserver.itb.cnr.it/vispa

Scientific Paper at BMC Bioinformatics: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1937-9

What is this repository for?

• Quick summary Tool for the analysis of retroviral vector Integration Sites (IS).

• Version Vector Integration Site Parallel Analysis, Version 2.

How do I get set up?

The full research article describes the software and its procecures.

An easy configuration script will support users in the process of installation of VISPA2. Use the following command line statement that will guide you through the installation and set up (as root user):

Option 1 (deprecated)

If you have a Linux System (Debian based) with Python 2.7 and R 3 you can use the configuration script below:

cd vispa2
# get help from the configuration file
./config_vispa2.sh -h
# run the installation and configuration of the required tools and download the genome(s), 
# here hg19 (this option will also index the reference genome). 
# The script exploits reference genome common names, as reported in UCSC web 
# site http://hgdownload.soe.ucsc.edu/downloads.html#mouse. 
# Please, enable internet network connections to UCSC web site.
./config_vispa2.sh -s human -i hg19

Option 2 (standard install)

If you have a newer system please use Conda to install some important packages and comment in the configuration script the relative lines:

conda env create -f vispa2.yml

Change py interpreter in each py script used (/opt/anaconda3/envs/vispa2/bin/python2)

Install mysql and configure it:

	mysql -uroot -p -e "
		GRANT ALL PRIVILEGES ON *.* To 'vispa2'@'localhost' IDENTIFIED BY 'vispa2';
		GRANT SELECT ON *.* TO 'readonly'@'localhost' IDENTIFIED BY 'readonlypswd';
		GRANT ALL PRIVILEGES ON *.* TO 'andrea'@'localhost' IDENTIFIED BY 'andrea';

Details for the configuration and running:

• CreateMatrix, the program to generate the final matrix file of annotated IS sites.

• [Installation Test](use vispa2_sampleData.sh in testing folder) for automated test.

Test the usage

To run a sample dataset please use the template and data in testing folder.

Who do I talk to?

• Repo owner or admin Giulio Spinozzi ([email protected]), Andrea Calabria ([email protected])