First you are going to need to add your peripheral to the Linux device tree so that your Linux system knows it is there. I did a similar application with a Zynq 7000 Processing System. This is assuming your architecture allows your processor to speak directly with peripherals using Linux.
http://www.wiki.xilinx.com/Linux+I2C+Driver
This is the Xilinx resource. It has an example of adding an i2c device to the device tree to access using the Cadence I2C driver. The Cadence I2C driver is used on a number of platforms. You should check for the Humming Bird Pro driver compatibility.
I assume you want to use the Linux I2C device interface. This is the approach I used and I assume it is the simplest. I would suggest you look at this to get an idea for what is involved on the software side.
http://rts.lab.asu.edu/web_438/CSE438_598_slides_yhlee/438_6_Linux_I2C_SMBus.pdf
I will assume you know the difference between the user space and the kernel space and how to use device drivers in user space applications. If not, I would suggest you take a look at these Xilinx resources that I think do an excellent job of covering the topic for embedded software designers.
https://forums.xilinx.com/xlnx/attachments/xlnx/ELINUX/10657/2/drivers-session3-uio-4public.pdf