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Going to Jerusalem by public transport is very easy. The train station (HaShmona) is just outside the port exit. Buy a ticket to Tel-Aviv (ask for a reserved seat) and get off at the Savidor Centre station. You exit via the bridge over the expressway that goes to the WEST and the bus terminal is 100 ft in front of you. Go to the last platform and take the #480 bus (they leave every 15-20 minutes). The bus takes you to the Central Bus Station in Jerusalem. From there you can take a taxi/tram/bus to your hotel.

Train schedules:

http://www.rail.co.il/EN/Pages/HomePage.aspx

A view of Savidor station and bridge over expressway (going west):

http://goo.gl/maps/SVSC7

Exit from the train station (via the turnstiles on the left side of the building):

http://goo.gl/maps/85eSM

Rotate the picture to the left (turn the wheel in the top-left corner) and you will see the entrance to the bus station:

http://goo.gl/maps/26WjU

And finally, a #480 leaving the bus station:

http://goo.gl/maps/z7p7F

Do NOT take the train all the way to Jerusalem. You will waste over an hour and end up on the wrong side of Jerusalem.