How to write an academic paper for the first time?
A book or paper on writing is a good introduction but can usually not solve everything. Reading a book does not mean you can reproduce what it teaches, particularly with writing since it is something that needs lots of practise. One problem is that writing is a question of both knowing how to structure the science but also a question of building and formulating the text, the latter being a language issue. So it is usually relatively easy to teach students how the technical side works and provide explanations for why. Teaching students how to be concise and precise is another question and without lots of practise it is quite difficult to get anywhere. During a thesis much of the language issues are ironed out by constant revisions sugested by the advisor. I also point out to all my students that writing is a life-long learning process and thatit is never to late to develop and change your writing.
However, I have some sources I fall back to:

Katz, M.J. From research to manuscript. A guide to scientific writing. Springer
Day, R.A. and Gastel, B., How to write and publish a scientific paper. Cambridge

The Purdue Online Writing Laboratory OWL is also very useful.
For language (English) I have (aside of Strunk &amp; White) found

Glasman-Deal, H. Science research writing for non-native speakers of English

of use.
There are of course lots of books around but all are definitely not good.
A final gem is a short paper on abstracts

Landes, K., A scrutiny of the abstract. Bulletin Of The American Association Of Petroleum Geologists. 50 (9), 1992-1999.

Which provides an excellent description of the abstract.