Installation Notes

• Make disease book run (create database and then run) :
  • As root user in mysql :
    • mysql> create database syndromebooktest_db; grant all privileges on syndromebook
    • test_db.* to molgenis@localhost identified by 'molgenis'; flush privileges; -- Query OK, 1 row affected (0.00 sec)
      • After this syndromebooktest_db is visible as molgenis user.
  • To run need molgenis3_3:
    • Disease book succesfully run . !
• DiseaseBook? model : available in html & dot , but no images available --> download graphiz :
  • how to create the images for the data model with ​Graphviz:
    • according to this : ​http://www.molgenis.org/wiki/TracWorkflow , ​http://www.molgenis.org/wiki/MolgenisOnWindows
      • we just need the dot files .
      • install graphviz & fix PATH: set to run 'dot.exe' from the commandline. In windows this is set in the control panel → System → Environment variables.:
        • Open graphviz : open dot files --> run ! --> Save As .. *
• new workspace: with mark' model :
  • changes in model:
    • login --> user .. later we can add authentication of molgenis (need the specific database table..)
    • syndrome --> patient
    • Gene --> Gene
    • OntologySource? --> OntologySource?
    • OntologyTerm? --> OntologyTerm? *
• Actions :
  • chat with Arthur Kuipers
    • are there any example data . We have available a potential format : ​http://localhost:8080/hvp_pilot/generated-doc/fileformat.html
    • Mark Kiestra : is here a mysql dump for disease book .
      • are there samples of real data --> mail to Mark ..done !
    • if Mark hasn't any available data refer to Rolf. *
• MacBook? :
  • Install tomcat ​http://www.malisphoto.com/tips/tomcatonosx.html
  • Setting environment variables : ​http://mactip.blogspot.com/2004/04/setting-environment-variables.html
  • Use Macports to install mysql : ​http://www.malisphoto.com/tips/mysql-on-os-x.html *