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Its a 2 TB Western Digital USB3.0 3.5" drive, nothing fancy but its in an external case and requires power.

I want to partition it for a hidden from windows Ubuntu Desktop 256GB and the rest a windows/linux accesable partition for Music and Videos so pretty much large files I will also be backing up my windows to that partition.
I want to install it without my Windows SSDs plugged in and I want to boot right past it unless I mash the boot select menu, in other words keep fast boot enabled.

Regarding hiding the partition from windows, I dont want windows to hide it as I am pretty sure that wont protect it against windows-linux trojans and ransomware etc
http://askubuntu.com/questions/289533/hide-ubuntu-partition-in-win7

So I pretty much want to hide it from Windows disk management.

My motherboard is an MSI Z170a Xpower Titnanium with the latest firmware. Running windows 7 x64

Stuff I have on bootable USB:
ctrl+f and ctrl+mousewheel recomended

Quote:
Clonezilla GPL Included in Parted Magic.
CopyWipe 1.14
EaseUs Disk Copy 2.3.1
g4u 2.5 BSD
HDClone (Free Edition) 5.1.5
partimage 0.6.9 GPL Included in Parted Magic
Partition Saving 4.20
PC INSPECTOR clone-maxx 1.0 Freeware Actual version is 0.95 Build 769, but is referred to as 1.0 on product website.
Q&D Unit Clone 1.1m
Cute Partition Manager 0.9.8
Dsrfix 3.12
FIPS 2.0 GPL
Free FDISK 1.3.1 GPL
GParted 0.13.1-git GPL Included in Parted Magic.
Partinfo 1.14 Freeware V1.11 and above are Windows only.
Partition Explorer 1.01
Partition Resizer 1.3.4
Partition Saving 4.20
PTDD Super Fdisk 1.0
Ranish Partition Manager 2.40 Freeware Using stable version because V2.44 is beta and reported to be buggy.
SPFDISK (Special FDISK) 2000-03v
XFDISK (Extended FDISK) 0.9.3 beta
Quote:
Data Lifeguard Tools (Western Digital) 11.2 Freeware
DiscWizard 2003 (Seagate) 10.45.06 Freeware
DiscWizard (Seagate/Maxtor) 11.0.8326 Freeware MaxBlast V5.0 is essentially the same thing i.e. OEM version of Acronis TrueImage. Startup Recovery Manager not included. Didn't see much use for it on the bootable CD, plus it can be activated in the Win32 program itself if required, or you can copy over the "Recovery Manager" folder youself.
Disk Manager (IBM) 9.61 Freeware
Disk Manager (Samsung) 10.42 Freeware
MaxBlast (Maxtor) 4.0 Freeware

Active Kill Disk 4.1.2393: Securely overwrites and destroys all data on physical drive (Dos Freeware).
CrystalDiskInfo 4.0.1: HDD health monitoring utility, displays basic HDD information, monitors S.M.A.R.T. values and disk temperature (Windows Freeware).
Darik's Boot and Nuke (DBAN) 1.0.7: Completely deletes the contents of any hard disk it can detect (Linux Freeware).
DRevitalize 1.2: Repairs bad sectors (physical defects) on hard drives by generating a special sequence of high and low signals around the physically damaged area (Dos Freeware).
DiskView 2.4: View graphical map of your disk, allowing you to check where a file is located or, by clicking on a cluster, seeing which file occupies it (Windows Freeware).
DiskWipe 1.2: Securely erases the contents of a disk replacing it with random data or leaving the drive completely blank (Windows Freeware).
ExcelStor's ESTest 4.50: ExcelStor hard disk diagnostic utility (Dos Freeware).
Gateway GwScan 5.12: Gateway hard drive diagnostic utility (Dos Freeware).
Hard Disk Sentinel 1.00.5: Hard Disk health, performance and temperature monitoring tool (Dos Freeware).
HDTune 2.55: HD Tune is a hard disk health, benchmarking, error scanner and information tool (Windows Freeware).
HDAT2 4.9B1: The main function is testing and repair (regenerates) bad sectors for detected devices. A freeware alternative of HDD Regenerator (Dos Freeware).
HDD Capacity Restore 1.2: This tool allows you to restore factory capacity of any hard drive. it does not read from or write to the user data area or perform any kind of formatting, only alters HDD firmware (HPA and DCO settings) (Windows Freeware).
MHDD 4.6: Precise diagnostic of the mechanical part of a drive, perform Low-level format, Bad Sector Sepair, access raw sectors, manage S.M.A.R.T (SMART) and other drive parameters such as acoustic management, security, Host Protected Area, etc. (Dos Freeware).
Samsung Disk Diagnose (SHDIAG) 1.28: Diagnose the disk when suspected to have failures (Dos Freeware).
Samsung ESTOOL 3.01v: Drive Diagnostic, Automatic Acoustic Management, Enable/Disable SMART etc (Dos Freeware).
Samsung HDD Utility(HUTIL) 2.10: The Drive Diagnostic Utility (Dos Freeware).
SeaTools for Dos: GUI 2.23 Text 1.10 versions to test Seagate or Maxtor Parallel ATA (PATA and IDE) and Serial ATA (SATA) interface disc drives (Dos Freeware).
SmartUDM 2.00: Hard Disk Drive S.M.A.R.T. Viewer (Dos Freeware).
Toshiba Hard Disk Diagnostic 2.00b: Toshiba hard drive diagnostic utility (Dos Freeware).
Victoria 3.33e and 3.52rus: a freeware program for low-level HDD diagnostics (Dos Freeware).
Victoria 4.46: Universal program for testing storage devices (Windows Freeware)
ViVard 1.0: HDD low-level diagnostics, Surface test with remap, SMART-attributes etc (Dos Freeware).
WDClear 1.30: Restore/Erases the drive back to a factory condition (Dos Freeware).
WDIDLE3 1.05: Modifies the behavior of a Western Digital Green drive to wait longer before positioning the heads in their park position and turning off unnecessary electronics (Dos Freeware).
Western Digital Data Lifeguard Tools 11.2: For the installation of Western Digital EIDE Hard Drives (Dos Freeware).
Western Digital Diagnostics (DLGDIAG) 5.19: Quickly and efficiently verify the status of the drive (Dos Freeware).
Western Digital Data Lifeguard Tools 1.24: Perform drive identification, diagnostics, and repairs on most WD drives (Windows Freeware)
MBR (Master Boot Record) Tools
BellaVista 1.1.0.71: Formerly BCD Editor with lots of options to configure Windows for a developer (Windows Freeware).
BootFix Utility: Run this utility if you get 'Invalid system disk' message (Dos Freeware).
BootSect 6.0.6: Boot Sector Manipulation Tool, This tool replaces FixFAT.exe and FixNTFS.exe (Windows Freeware).
BootICE 2012.09.20: A boot sector manipulation utility to edit MBR/PBR/BCD (Windows Freeware).
DiskMan 4.2: All in one tool for cmos, bios, bootrecord and more (Windows/Dos Freeware).
FbInst 1.6: A tool to create universal flash boot disk that boots from all computers (Windows Freeware).
Grub4Dos installer 1.1: An universal boot loader GRUB for DOS GRLDR installer (Windows Freeware).
grub4dos 2012-10-02: An universal boot loader based on GNU GRUB, can boot off DOS/LINUX or via Windows boot manager/syslinux/lilo or from MBR/CD, builtin BIOS disk emulation (Linux Freeware).
HDHacker 1.4: Load/Save/View MBR and BootSector from a physical/logical drive (Windows Freeware).
isolinux 4.05: A boot loader for Linux/i386 that operates off ISO 9660/El Torito CD-ROMs in 'no emulation' mode (Linux Freeware).
MBRWizard 3.0.73: Directly update and modify the Master Boot Record (Windows/Dos Freeware).
MbrFix 1.3: Backup, restore and fix the boot code in the MBR (Windows/Dos Freeware).
MBR Utility 1.05: Manipulate a drive's master boot record (MBR) via the command line (Windows/Dos Freeware).
MBRWork 1.08: A utility to perform some common and uncommon MBR functions (Dos Freeware).
MBRTool 2.3.200: Backup, verify, restore, edit, refresh, remove, display, re-write and more (Dos Freeware).
MBR SAVE / RESTORE 2.1: BootSave and BootRest tools to save / restore MBR (Dos Freeware).
MemDisk 4.05: Allow booting legacy operating systems, floppy images, hard disk images and some ISO images (Linux Freeware).
PLoP Boot Manager 5.0.14: Boot different operating systems harddisk, floppy, CD/DVD or from USB, it can boot from an USB/CD/DVD even without BIOS support (Linux Freeware).
RMPrepUSB 2.1.620: Partition and format your USB drive and make it bootable (Windows Freeware).
Smart Boot Manager 3.7.1: A multi boot manager (Linux/Dos Freeware).
XOSL 1.1.5: A graphical boot manager that supports multi-booting of various operating systems (Dos Freeware).[/QUOTE]
 

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You are on right track, just install some linux disto like Lubuntu from bootable usb key. To leave system disk with Windows intact unplug drive during installation. Windows will not be able to read from ext4 partition which will be positioned on external drive unless you install special driver inside windows.

Downside of this portable linux is that you need to select in bios bootable device, the plus is that you can port it anywhere.

If you want second partition with music, etc on external drive, just shrink free space with gparted or other partition tool and create new ntfs partition (that will be accessable in both windows and linux world). But don't complicate too much - external hard drives are very cheap thesedays.
 
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