UROPA GUI: A Web Platform for genomic region annotation

The annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with crucial impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which considerably extends the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.

Features

• Input: BED file of peaks or other genomic regions
• Reference: GTF file of desired target features (e.g. genes, transcripts, probes, repeats, ...); source = Gencode/Ensembl (102 organisms included) or custom upload
• Association rules: VERY diverse and easily combinable to a complex ruleset
• Persistence: Unique identifier is created on the server and results will remain available temporarily using the respective link
• Hosted: Either online on our web server or as a local R Shiny installation

Availability and Implementation

The open source UROPA GUI server was implemented in R Shiny and Python and is available from http://loosolab.mpi-bn.mpg.de/.

The source code of the underlying UROPA command line application can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA under the MIT license.

An exhaustive manual can be found at https://uropa-manual.readthedocs.io/.

Please make sure to check our other projects at http://loosolab.mpi-bn.mpg.de/.

Try UROPA GUI

The web server contains all necessary data to quickly sample the capabilities of UROPA GUI.

• UROPA user guide: Stepwise tutorial.
• Example data: Select "Load Test Data" and "Run UROPA".

Installation of UROPA GUI in “virgin” Debian 9 Linux

Update and install the following Debian packages.

sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get install r-base libnlopt-dev wget libssl-dev libxml2-dev libcurl4-openssl-dev git gdebi-core

Install R Shiny server according to the manual found here https://www.rstudio.com/products/shiny/download-server/ (make sure to install to global R library, NOT personal!).

Install Miniconda3 according to the manual found here https://conda.io/miniconda.html. Include the Path to the miniconda3/bin folder in both: /home//.bashrc and /home//.profile.

export PATH="/home/bioi/miniconda3/bin:$PATH"

Install UROPA using pip.

pip install --pre uropa

Get the R Shiny application UROPA GUI from Github.

git clone https://github.molgen.mpg.de/loosolab/UROPA_GUI

Copy the UROPA_GUI subfolder to the desired R Shiny application folder (ex. /srv/shiny-server/apps).

Change the owner of the R Shiny apps folder to be the “shiny” user.

sudo chown –R shiny:shiny /srv/shiny-server/apps 

Restart R Shiny server.

sudo systemctl stop shiny-server
sudo systemctl daemon-reload
sudo systemctl start shiny-server

Install nginx.

sudo apt-get install nginx
sudo systemctl start nginx.service
sudo systemctl enable nginx.service

Install php5-fpm.

sudo apt-get install php5-fpm
sudo systemctl start php5-fpm
sudo systemctl enable php5-fpm

Configure php.ini.

sudo nano /etc/php5/fpm/php.ini
cgi.fix_pathinfo=0

Restart php5-fpm.

sudo systemctl restart php5-fpm

Configure nginx.

sudo nano /etc/nginx/sites-available/default
server {
    listen 8080 default_server;
    listen [::]:8080 default_server;
 
    root /var/www/html;
    index index.php index.html index.htm index.nginx-debian.html;
 
    server_name your_server_ip; //enter the IP of the server here!!!
 
    location / {
        try_files $uri $uri/ =404;
    }
 
    location ~ \.php$ {
        include snippets/fastcgi-php.conf;
        fastcgi_pass unix:/var/run/php5-fpm.sock;
    }
 
    location ~ /\.ht {
        deny all;
    }
}

Restart nginx.

sudo sytemctl restart nginx.service

Create symbolic link for UROPA in the /var/www/html folder.

sudo ln -s /opt/uropa/apps/UROPA_GUI /var/www/html/UROPA_GUI

How to cite

• Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: https://www.nature.com/articles/s41598-017-02464-y

• Hendrik Schultheis, Jens Preussner, Annika Fust, Mette Bentsen, Carsten Kuenne, Mario Looso: UROPA: A Web Platform for genomic region annotation

License

This project is licensed under the MIT license.