Jose,
Most git hooks should work in MyEclipse, though there are reports about some hooks like update not working as expected in Eclipse.
Please refer to this bug report about Git hooks in Eclipse for more details and see if the suggested workarounds help fix the problem at your end : https://bugs.eclipse.org/bugs/show_bug.cgi?id=493721
The git support in MyEclipse is the same as Eclipse’s eGit tooling which we integrate, so the same documentation and instructions would apply in MyEclipse as well.
Apologies for inconvenience caused. Please let us know if you have any further questions.
–Swapna
MyEclipse Support