wiki:biobase

Transfac and Transpath

The department has a academic license for Transfac and Transpath. The license grants us to use the tools within our project group.

You need a password to access Transpath or Transfac. This password can be acquired from the maintainer of the installation.

The database update service expires May 31, 2008.

Package maintenance information

Current maintainers are Jari and Mattias.

The server is installed on tom.thep.lu.se bioinfo.thep.lu.se. All links to tom.thep.lu.se should be replaced with bioinfo.thep.lu.se.

Upgrade

This follow the installation path outlined below. This is a short ouline of the steps

  • Download.
  • Install with perl install_linux.pl.
  • Replace .htaccess, hosts.list, and user.list, with symbolic links (see below)
  • Edit /etc/apache2/httpd.conf.local, search for transfac/transpath, change version number.
  • Restart apache, /etc/init.d/httpd restart.
  • Check the new version transfac and transpath
  • Remove the old version from the server. Older versions are currently saved in /scratch/lev/jari/biobase.

First time install

Download the latest version of the applications, you'll need a user-id and password.

Follow the instructions in the package README.txt. This is basically that you do perl install.pl and answer the questions. The current apache has /srv/www as SERVER_ROOT, and the rest is basically to accept the defaults.

Web server configuration

The databases works with both Apache version 1 and 2, the changes in the configuration files are similar.

We are running Apache 2 (SuSE install).

The installation creates the entry point that looks like http://bioinfo.thep.lu.se/cgi-bin/biobase/transfac/11.1/bin/start.cgi, but to make things easier for the users I make apache to do an automatic redirect from http://bioinfo.thep.lu.se/transfac/ to the valid entry point. This is simply done with a line

Redirect /transfac http://bioinfo.thep.lu.se/cgi-bin/biobase/transfac/11.1/bin/start.cgi

in the appropriate config file (/etc/apache2/http.conf.local on SuSE with proper apache setup). For transpath and other versions the needed changes should be obvious.

Access configuration

Since we have several databases from BIOBASE the access configuration is somewhat different from what is described in the documentation provided with the databases. The scheme outline below will use the same access files for all BIOBASE databases.

Host (client) access configuration
First move the template hosts.list installed during installation according to the example below, and replace the template with a symbolic link (transpath does not come with the etc directory, just omit it and things should work)

cd /srv/www/cgi-bin/biobase
mv transfac/11.1/etc/conf/hosts.list .
cd transfac/11.1/etc/conf
ln -s ../../../../hosts.list

If you loose this file it is easy to recreate. The file is a list of ip numbers (one at each row) of the clients that is allowed to use the databases. Wildcards like 130.235.95.* can be used.

User access configurarion
First move the templates .htaccess and user.list according to the example below, and replace the templates with symbolic links

cd /usr/local_local/packages/apache/cgi-bin/biobase
mv transfac/7.4/bin/.htaccess .
mv transfac/7.4/bin/user.list .
cd transfac/7.4/bin/
ln -s ../../../.htaccess
ln -s ../../../user.list

Then you need to change the reference to user.list in .httaccess, and finally add users with

cd /srv/www/cgi-bin/biobase
htpasswd2 -b user.list user password
Last modified 9 years ago Last modified on Feb 21, 2008, 2:48:48 PM