It depends on how you are authenticating to that SQL server. If you are trying to use the integrated authentication (where the login to SQL is handled by the user starting the application/service rather than the values defined in the dbconfig.xml), then I have not seen this to be possible yet on a non-microsoft operating system (such as any linux/unix platform) when using the Microsoft database driver with Jira.
The use of the Microsoft driver I believe will exclude linux environments from being able to use the integrated authentication feature.
If you really want to use this authentication method for Jira to a MS SQL database, I would actually recommend using the Microsoft driver on a windows platform. All versions of Jira from 7.5 and higher will use this database driver by default.
We have a KB that explains the steps needed to configure this setup in Using Integrated Security with MsSQL for Jira.
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