How to flash zip on Genymotion programmatically

Paul's answer is good.

Also, we will soon release features related to continuous integration and automation. A command line tool will be included on these features. It allows you to do all what you can do with your mouse, but through the command line. It will be available to paid licenses.

You can find a demo we did at Droidcon Paris here.

Genymotion VMs contain some special scripts that interface with their launcher and skin controls. The one that you need is /system/bin/flash-archive.sh which is what gets run when you drag & drop a .zip archive.

You can run flash-archive.sh directly using ADB or from a process within the VM. So if you have the zip in /sdcard/Download/gapps.zip, you can run the following command from the host machine:

adb shell flash-archive.sh /sdcard/Download/gapps.zip
adb reboot

Don't forget to install the ARM translation package first, if applicable. It can be done using the same sequence.