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So my configuration is such that my windows 7 is installed on a msata ssd drive and I am trying to install ubuntu on my regular sata hdd. Overall the windows installer copies the files but ubuntu doesn't show in the boot menu. Could you tell me the solution for that?

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Are you using WUBI.EXE to install Ubuntu from within Windows, or are you booting from a Live USB/DVD and installing from there using the side-by-side option? –  user68186 Mar 15 '13 at 19:58
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2 Answers

You need to use grub, its a boot manager. It will load a list of boot options eg win 7 win 8 ubunutu.

However grub works on a linux system, and your MBR (master boot record) is on the windows drive. So windows boots before even know there are other drives with other options.

for safety sake I say tell your bios to boot the sata hdd first, you will then need to configure grub to offer the option to boot the ssd.

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My installation scenario is very similar to yours, Win7 On SSD, and Ubuntu 12.10 on an internal SATA drive. When I installed Ubuntu I opted to manually partition the HDD.
After installation I changed my bios to boot from HDD; since there are 2 distinct OSes installed GRUB presents the option to boot Ubuntu (1st option) or Win 7 (second option) without having to mess with bios settings. If you wish to have Win 7 as the first option (therby after a short timeout GRUB will automatically boot Win 7 - Grub Customizer is available for installation

sudo add-apt-repository ppa:danielrichter2007/grub-customizer
sudo apt-get update
sudo apt-get install grub-customizer
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