Frequently Asked Questions
For version 12.5, the database management system for storing GeneSpring data (e.g. experiments, analysis results, annotations, pathway-related databases) was changed from MySQL to PostgreSQL. Therefore, all the existing data has to be migrated from the MySQL database to the PostgreSQL database before you can start working with GeneSpring again. Depending on the size of your data (for example if you have previously downloaded interaction databases of multiple organisms), this process can take several hours.
The information dialog guiding you through the update and migration process provides estimated size requirements and informs you if the available space in the GeneSpring installation directory is not sufficient. PostgreSQL migration involves copying the entire MySQL folder. The MySQL folder will remain untouched after migration. This means, if the MySQL folder occupies x GB space, you will need at least twice that amount (2x) plus some extra space, which varies, but is typically around 10% of the size of the original MySQL folder (10% of x). Therefore the total space requirement is approximately 2.1x.
There are a number of reasons why the PostgreSQL database would have failed to startup, which can depend on your system specifications:
1) All supported systems (Windows, Mac, or Linux): The GeneSpring PostgreSQL database uses a fixed port to run (port 5435). If any other application on your computer is using the same port at the time you started GeneSpring, the PostgreSQL database will not have been able to startup. You can resolve this issue by opening the following file in the GeneSpring installation directory in a plain text editor (like Wordpad):
In the file, use the Find function to go to the following phrase: "port = 5435" and change this number to 543x, where x is greater than 5. Save the file and launch GeneSpring again.
Note: Not all applications use fixed ports, but might randomly choose a free port to run. Or you might install another application that uses the same port as GeneSpring’s PostgreSQL database. Therefore, this issue can occur again at a later time, even if you have changed the port once. If this is the case, just repeat the instructions here to change the port again.
2) Mac or Linux machines: You might not have the required permissions to start the PostgreSQL database. For these types of machines, PostgreSQL requires the ‘700 file permission’. You can manually change the permission settings using the chmod command. In the Command Prompt, point to the ‘app’ folder in the GeneSpring installation directory and execute the following command: ‘chmod-R 700 PostgreSQL’. This will set the permissions for you to have read, write to, and execute permissions for the PostgreSQL folder. This process only has to be executed once. If this does not resolve the issue, try changing the port for the PostgreSQL database as described in 1).
3) Linux 64-bit operating systems only: In addition to the standard libraries, the PostgreSQL database requires the “ia32-libs” package to startup. Contact your system administrator to install the package or contact GeneSpring support. This process only has to be executed once. If this does not resolve the issue, try changing the port for the PostgreSQL database as described in 1).
If none of these options resolve the issue, please contact GeneSpring support for further assistance.