I have struggled a lot with the thesis format and never really found a format that works smoothly. Either tikz doesn’t work or wrapfig, and throws up a large amount of errors. If you want to make your thesis look nice and beautiful, I’m afraid you need to use packages like tikz, color, graphicx, hyperref, breakurl etc. So, the native IISc thesis was incompatible with all of them. In particular, it creates a pretty bland form of the thesis which is a pain to read online. Remember for online viewing (which happens most often in the web these days), you need to have a nice navigation, and that means you should have hyperlinking within the document. It is always useful if I can click from the contents page and land up to the place what I wanted to read. So, I thought of hacking a bit on the template and here is the bundle for LaTeX which you can use to create such a file.
It is quite self-explanatory. Just write your chapters separately and save as corresponding .tex files and include in the thesis.tex file and compile the thesis.tex. For an aid, I have put a script file in the archive, so that you can just run ./script on the terminal and it will generate the thesis.pdf. If the script is not executable, change the mode. Open a terminal, and type the following.
chmod 777 script
If everything goes okay, you should be on the top of your thesis, congratulations! You should be able to generate this document. Just go to the contents page and click on the page numbers, and then you’ll appreciate all that I was talking about. Good luck!
Like this page if you find it useful, also let me know if there are any troubles with the file.
A bit of self advertisement: I made my thesis using this template.