EMMA 2 Getting Started

Here comes a short HowTo about how to get started with developing EMMA.

CVS

• create a working direktory for CVS in your home named 'CVS'
• cd to that directory and get the projects needed to run emma:

cvs checkout bioinfo/emma2

  you need to checkout the following projects:

• emma2
• projectmanagement
• common

Web-Server

• goto CVS/bioinfo/emma2/share/www
• edit apache2.sh: change PORT=XXXX to any free port on the webserver, and set CVS= to your CVS-directory
• login on the testwebserver (hook): `rsh hook`
• execute

CVS/bioinfo/emma2/share/www/apache2.sh start

• try to open http://hook:PORT with your browser
• if nothing happens or you get an error message have a look at `CVS/bioinfo/emma2/share/www/all.errors`

Documentation

The main source of documentation is this Wiki ;) see EMMA2Overview The other main source is the perldoc documentation. The generated O2DBI-servermodules are pod documented you can read with:

perldoc module.pm

Other modules may also have pod-documetation but this is not guaranteed. The documentation found can also be incomplete or rather outdated. The documentation of the server-modules is mostly derived from the MAGE-OM documentation. Additional documention on the MAGE-OM part of the data scheme can be found at http://www.mged.org .

Additional documentation can be found in CVS/bioinfo/emma2/share/doc.

Directory Structure

The directory `CVS/bioinfo/emma2/` contains the specific components of the emma2 software:

• `/bin` start wrapper(s) for executable scripts in `/share/exec`.

To run a script in share exec type: `emma_start scriptname.pl -p project [options]`

• `/share` contains the main application code
  • `/exec` executable scripts
  • `/perl` contains the perl code
    • `/EMMA` same as above
      • `/www/modules` modules generating html
      • `/www/cgi-bin` the cgi-scripts
      • `/DBmodules` modules accessing the backend, used by the www-modules
      • `/MAGEOM` the generated o2dbi backend modules
      • `/MAGEOM_Server` the extension modules for o2dbi where functionality can be added to the standard classes
• `/www` contains web-server specific code and the document root
  • `/tmpl' the HTML-templates for each page
• `/src` contains the DB scheme and code for generation of code and documentation