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## 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]( https://uropa-manual.readthedocs.io/config.html) | |
- **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](http://loosolab.mpi-bn.mpg.de/) 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/<USER>/.bashrc and /home/<USER>/.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. |