Reddit reviews Linux Programming by Example: The Fundamentals (Prentice Hall Open Source Software Development)
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Linux e-book is a very broad subject. Maybe I could make some recommendations if you wanted to narrow it down a bit?
edit: for a good "linux" book i've heard good things about Linux Programming By Example: The Fundamentals.
http://www.amazon.com/Linux-Programming-Example-The-Fundamentals/dp/0131429647/ref=pd_sim_b_7
C, C++, Assembly are best suited for the purpose. For managed code rootktis part, learn Java and/or .NET.
For Linux programming, have a look at (http://www.amazon.com/Linux-Programming-Interface-System-Handbook/dp/1593272200/ref=sr_1_1?s=books&ie=UTF8&qid=1450511098&sr=1-1&keywords=LINUX+Programming). In fact, this is a must read book IMHO. Apart from this, you can try these too:
EDIT: Formatting
A good book on the subject of command line programs is Linux Programming By Example.
A good site on sdl and basic graphical programming for linux is: Lazyfoo. Of course, OpenGL is another choice, and programming in OpenGL is basically the same cross platform.
The best book if you plan to start working on the kernel (in my opinion) is actually the Device Driver Book, but people also really like the Understanding the Linux Kernel book.
Obviously the other option is just looking for good tutorials online, for that you need:
gcc
tutorialC
tutorialmake
tutorialgdb
andddd
tutorialOf course there's also Qt which is used by a lot of people.