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A Guide to Writing Your Thesis Using LATEX

Generating the Thesis

The steps for generating the thesis were given in The Template Files, but here we will discuss the steps in a little more detail. Because the steps are different on different operating systems, we will again discuss them separately.

Generating the Thesis in UNIX

From a command prompt, such as a terminal program like xterm, go to the directory that contains the thesis. This is the directory where you will run all of your commands. To update thesis.pdf with the changes that you have made, type the command: 

  pdflatex thesis.tex
then open up thesis.pdf in a .pdf viewer. Most .pdf viewers have the ability to reload the modified file without closing the viewer, which can be convenient while writing the thesis, so if it is already open in a viewer, just reload it.

Besides pdflatex, which generates the thesis, the other command that you will need to use is 

  sh genbib.bat
which will update the bibliography and list of references. This command only needs to be run after you have added a new citation. Note that you never need to run bibtex explicitly, the script genbib.bat takes care of it for you.

To ensure that all labels, lists of references, the bibliography, the list of tables, the list of figures, and the table of contents are up to date, such as for a final copy of your thesis, you can run the sequence of commands 

  pdflatex thesis.tex
  sh genbib.bat
  pdflatex thesis.tex
  pdflatex thesis.tex
and it will ensure that everything is up to date.

Sometimes an error in one of your .tex files can corrupt one of the auxiliary files created by LaTeX. It is always okay to delete any of these auxiliary files, as they will always be recreated. The file extensions that can be safely deleted include .aux, .bbl, .blg, .log, .lot, .lof, .toc, and .out. To remove all of the .aux files, which are usually the problem, type the command 

  rm *.aux

Generating the thesis in Windows

In WinEdt, open the thesis.tex. This is the only file which you will need to run LaTeX on. To update and display the thesis.pdf file

  • press the button ``PDF TeXify''.
This will run pdflatex on the thesis, and start or reload the .pdf viewer. Whenever you make changes to any of the .tex files, you still only run ``PDF TeXify'' on the file thesis.tex.

To update the bibliography and lists of references

  • press the button ``Run...'', then run the command genbib.bat
This command only needs to be run after you have added a new citation. Note that you never need to run bibtex explicitly, the script genbib.bat takes care of it for you.

To ensure that all labels, lists of references, the bibliography, the list of tables, the list of figures, and the table of contents are up to date, such as for a final copy of your thesis, you can run the following sequence of commands in WinEdt. Open the file thesis.tex in WinEdt, then

  • press the button ``PDF LaTeX''
  • press the button ``Run...'', then run the command genbib.bat
  • press the button ``PDF LaTeX''
  • press the button ``PDF LaTeX''
This will ensure that everything is up to date in the thesis.

Sometimes an error in one of your .tex files can corrupt one of the auxiliary files created by LaTeX. It is always okay to delete any of these auxiliary files, as they will always be recreated. The file extensions that can be safely deleted include .aux, .bbl, .blg, .log, .lot, .lof, .toc, and .out. In WinEdt, there is an icon of a recycle bin called "Erase Working Files". Clicking on this icon will remove all of these files for you.