SHAPEwarp-web

SHAPEwarp-web is a web user interface to the SHAPEwarp algorithm for RNA structure homology search.

Requirements

RNAFramework v2.8.7 or greater (https://github.com/dincarnato/RNAFramework/)
SHAPEwarp v1.2 or greater (https://github.com/dincarnato/SHAPEwarp/)
R2DT v1.4 (https://github.com/RNAcentral/R2DT), installed as a Singularity image (please refer to the installation manual)
A webserver (such as Apache)

The path to the RNA Framework's lib/ folder must be added to the PERL5LIB environment variable of the user running the webserver process (typically apache or www-data). Alternatively, the path can be manually changed inside the results.cgi and shapewarp.cgi scripts (located under scripts/), by amending the following line:

# Change to reflect the actual path to RNA Framework's lib/
use lib "/var/www/html/shapewarp/scripts/lib";

## Configuration A number of parameters, including the path to the SHAPEwarp executable and to the R2DT Singularity image, can be specified in the `shapewarp.conf` file.

Parameter names are case sensitive. Parameter/value pairs must be separated by the = sign (no spaces):

# SHAPEwarp Configuration File
#
# Parameter           Description
# =========           ===========
# swPath              Full path to the SHAPEwarp executable (if not provided, will assume it is in PATH)
# r2dtPath            Full path to the R2DT Singularity image
# msDelay             Refresh frequency (in millisec)
# maxQueryLen         Maximum allowed length of a single query
# maxTotQueryLen      Maximum allowed cumulative length of multiple queries

swPath=/usr/local/bin/shapewarp-main/target/release/shapewarp
r2dtPath=/etc/r2dt
msDelay=5000
maxQueryLen=500
maxTotQueryLen=5000

Depending on the webserver used, the scripts/ folder might need to be configured to be granted CGI execution permissions. On Apache, this can be achieved by configuring a Virtual Host. For example:

<VirtualHost *:80>

  ...

  <Directory "/var/www/html/shapewarp/scripts/">
      Require all granted
      Options +ExecCGI
      AddHandler cgi-script .cgi
  </Directory>
  
</VirtualHost>

Furthermore, the ownership of the folder containing SHAPEwarp-web must be assigned to the user running the webserver. For example:

chown -R www-data:www-data shapewarp/
chmod -R 755 shapewarp/

dincarnato/SHAPEwarp-web

SHAPEwarp-web

Requirements