Fix travis build

Created by: mira13

Description

Fixing tests and travis build script. Befor in travia as a result was used variable that is always 0. So we had successful tests whatever is failed. After travis was fixed, it became obvious that some tests are not pasing, they are fixed as well - transcript, translation and gene tests. Few variables in sql requests were quoted, it doesn't make any difference in current sql, but makes code work in new sql server

detail of the fix: before, we took as a result last command output - $? , Last tests command is perl test run inside if statement, so when after if we took $? - it was result of if, but not the test run inside. Eventually of if obviously is always 0.

Use case

Travis test result was sucsessful, even if tests fails

Benefits

We have correct test system.

Possible Drawbacks

Still few more fails of tests are not covered in this branch, so it will be futher work

Testing

Yes, all tests now correct and pass I have run all them localy and on server