| | 1 | == Installation Notes == |
| | 2 | * Make disease book run (create database and then run) : |
| | 3 | * As root user in mysql : |
| | 4 | * mysql> create database syndromebooktest_db; grant all privileges on syndromebook |
| | 5 | * test_db.* to molgenis@localhost identified by 'molgenis'; flush privileges; -- Query OK, 1 row affected (0.00 sec) |
| | 6 | * After this syndromebooktest_db is visible as molgenis user. |
| | 7 | * To run need molgenis3_3: |
| | 8 | * Disease book succesfully run . ! |
| | 9 | * DiseaseBook model : available in html & dot , but no images available --> download graphiz : |
| | 10 | * how to create the images for the data model with [http://www.graphviz.org/About.php Graphviz:] |
| | 11 | * according to this : http://www.molgenis.org/wiki/TracWorkflow , http://www.molgenis.org/wiki/MolgenisOnWindows |
| | 12 | * we just need the dot files . |
| | 13 | * install graphviz & fix PATH: set to run 'dot.exe' from the commandline. In windows this is set in the control panel → System → Environment variables.: |
| | 14 | * Open graphviz : open dot files --> run ! --> Save As .. * |
| | 15 | * new workspace: with mark' model : |
| | 16 | * changes in model: |
| | 17 | * login --> user .. later we can add authentication of molgenis (need the specific database table..) |
| | 18 | * syndrome --> patient |
| | 19 | * Gene --> Gene |
| | 20 | * OntologySource --> OntologySource |
| | 21 | * OntologyTerm --> OntologyTerm * |
| | 22 | * Actions : |
| | 23 | * chat with Arthur Kuipers |
| | 24 | * are there any example data . We have available a potential format : http://localhost:8080/hvp_pilot/generated-doc/fileformat.html |
| | 25 | * Mark Kiestra : is here a mysql dump for disease book . |
| | 26 | * are there samples of real data --> mail to Mark ..done ! |
| | 27 | * if Mark hasn't any available data refer to Rolf. * |
| | 28 | * MacBook : |
| | 29 | * Install tomcat http://www.malisphoto.com/tips/tomcatonosx.html |
| | 30 | * Setting environment variables : http://mactip.blogspot.com/2004/04/setting-environment-variables.html |
| | 31 | * Use Macports to install mysql : http://www.malisphoto.com/tips/mysql-on-os-x.html * |
