How to compile LaTeX file

How to compile LaTeX file
Here are the typical steps to produce DVI, PostScript or PDF file from a LaTeX source file:
1. Create the LaTeX source file. It must be in the plain ASCII format. Simple text editor like
Notepad, VIM or Emacs would be fine. Please do not use word processor like Microsoft
Office.
2. Run LaTeX on the LaTeX source. Any warning or error will be reported, if exists. If the
source file contains table of contents, or references, you may need to run the above
command several times. If you are lucky, you will get a DVI file, called yourfile.dvi. To
view it, use dvi viewer like xdvi or Yap.
latex yourfile.tex
3. To convert the DVI file to PostScript format, run
dvips -Pcmz yourfile.dvi -o yourfile.ps
4. To produce a PDF file, you don’t need to do step 1. Just run
pdflatex yourfile.tex
5. To produce a PostScript file from a PDF file,
pdf2ps yourfile.pdf newfile.ps
6. To produce a PDF file from a PostScript file,
pdf2ps yourfile.ps newfile.pdf

LaTeX for Beginners

Setting Up

Setting up LaTeX isn't too hard. You can learn about it from LaTeX Bibliography and other resources. Here are several methods I've used:

• Set it up using the T_EX Collection DVD from the TeX User's Group (TUG) for a Mac.
• A really easy way to get going: install a RedHat Linux. My Linux 7.1 had LaTeX already set up.
• These days I'm using Ubuntu Linux. It's not pre-installed but just type 'latex' and it will lead you to installation!

To test my LaTeX installation I typed in (or cut and paste) this small file:

\documentclass[12pt]{article}

\begin{document}

\large
a buncha
stuff

\begin{equation}
\sqrt{\pi}
\end{equation}

\end{document}

I called it test.tex. Then I did this:

latex test
xdvi test

The first line ran LaTeX and the second one poped up a viewer. It worked fine. On Ubuntu I also did:

latex test
dvips test
gv test.ps
ps2pdf test.ps

I found I needed to install gv - that took only a few seconds. So I was able to get LaTeX running on Ubuntu in about 5 minutes, mostly waiting for the download. The last step made a PDF for me and double clicking on it in the graphical window opened it in evince. Notes:

• A fully worked example is in latex.test. You can see the result in the test.png file, shown to the right. It's not very fancy, but you can go to The TeX showcase if you want fancy!
• In general one may need to call LaTeX several times to get cross references right.
• Actually, I put the two commands above into a file and used it as a script, in preparation for automating the whole process using atchange. This makes LaTeX into a WYSIWYG (what you see is what you want!).
• A more complex starting file and other paraphernalia is in this directory. It contains, among other things:
  • a LaTeX file, latexdemo.tex
  • the resulting dvi (device independent file), paper.dvi
  • the postscript created by topostscript: paper.ps
  • the PDF created by ps2pdf: paper.pdf

Some simple rules for typesetting in LaTeX:

• Get used to your text editor first. I like vi and vim, other people like emacs. The advantage of learning vi is that all unix operating systems have it. It's also quite ergonomic. Avoid using the arrow keys since they will not be available on all keyboards.
• In LaTeX, paragraphs are separated by blank lines. If you are using the vi editor, you can hop between paragraphs with "}" (move forward one paragraph) and "{" (move back one paragraph. You can also move paragraphs around. If you are above one paragraph, just d}p to switch it with the next paragraph!
• As in standard typing, sentences are separated by two spaces. If you are using the vi editor, you can hop between sentences with ")" (move forward one sentence) and "(" (move back one sentence. You can also move sentences around. If you are at the start of one sentence, just d)p to switch it with the next sentence!
• \emph{Italics} gives italics
• \textbf{Bold face} gives bold face
• lines that begin with a percent (%) are comment lines. They do not show up in the final text.
• \cite{Shannon1948} automatically (!) pulls in the citation for Shannon's famous 1948 paper (assuming you already have it in a database). Further details are beyond the scope of this page, but you can use atchange to automate the generation of the BiBTeX database.
• \command{argument} is the form of a command with its argument.
• Mathematics inside a line is surrounded by the $ symbol: $\sqrt{\pi}$ gives the square root of pi. Also \begin{equation} and \end{equation} surround larger equations, and these automatically (!) get numbered throughout the paper .
• Books
  • TeXbook by Donald Ervin Knuth. The original definition of TeX, upon which LaTeX was built. (This is the raw language components.)
  • LaTeX : A Documentation Preparation System User's Guide and Reference Manual by Leslie Lamport, Duane Bibby. The original definition of LaTeX, a macro system under TeX. (This is the easier to use language, but the book is hard to read.)
  • Guide to LATEX: Document Preparation for Beginners and Advanced Users by Helmut Kopka, Patrick W. Daly. VERY useful book.
  • The Latex Companion by Michel Goossens, et al. This is a good book about packages to do everything imaginable in typesetting.

---

Advanced stuff

• LaTeX Bibliography and other resources
• We use two definitions:
  • \newcommand{\todo}{\rule{0.5em}{1ex}}
    Having made this definition one just says: \todo. This just puts a black rectangle into the text. It is impossible to miss these. They makr places where we still need to do something.
  • \newcommand{\todobf}[1]{{\rule{0.5em}{1ex}\textbf{ #1}}}
    Having made this definition one says: \todobf{some stuff}. This will put the little black rectangle and "some stuff" in bold face. It's useful for writing down what we need to do at this point.
• tools that make LaTex into a wysiwyg
• Changing the Font. To change to the Times New Roman Font using LaTeX2e, before your \begin{document} put \usepackage{pslatex}. More on fonts.
• Making Figures. To make figures using LaTeX2e, before your \begin{document} put

  \usepackage{graphics}
  \usepackage{wrapfig}
  \usepackage{floatfig}
  

  Then call the graphics directly like this:

  \includegraphics*{fig/logowalker.ps}
  

  or inside a figure:

  \begin{figure}
  \begin{center}
  \scalebox
  {0.9} % h_length
  {
  \includegraphics*{fig/logowalker.ps}
  }
  \end{center}
  \caption{
  The caption
  }
  \label{fig.logowalker}
  \end{figure}
  

  The wrapfig and floatfig packages are very cool - they let you wrap figures around text. Between paragaphs:

  \begin{floatingfigure}{7 cm}
  \scalebox{0.6}{
  \includegraphics*[140,270][450,640]{fig/t7-wt-ex.ps}
  }
  \caption{Sequence logos for T7 promoters.
  Top: wild type promoters \cite{Schneider1986};
  bottom: strong T7 promoters found by an
  \emph{in vivo} genetic screen \cite{Schneider1989}.
  }
  \noindent \hrulefill
  \label{fig.t7-wt-ex}
  \end{floatingfigure}
  

  Wrap figure looks like this:

  \begin{wrapfigure}{r}{12cm}
  \begin{center}
  \rotatebox{-90}{
  \scalebox
  {0.57} % h_length
  {
  % Note: the "*" makes the graphic be clipped - this is needed!!
  % Guide to Latex p. 168
  \includegraphics*[50,110][540,695]{fig/baseflipcover.ps}
  }
  }
  \end{center}
  \caption{
  Anomalous base in RepA binding sites.
  Sequence logos for
  12 repressors and activators were created.
  The logos were
  then aligned so that the proteins would all be on
  the same face of the DNA.
  Since proteins make most of their contacts
  in major grooves, there are two highly conserved
  regions that correspond to two major grooves of
  DNA, shown on top.
  In addition, the sequence logo for
  bacteriophage P1 RepA protein binding sites
  was overlayed on top of the other sequence logos.
  An unusually conserved thymine (red T) in the middle of
  the RepA sites,
  dubbed ``Tom's T'' by Dhruba Chattoraj,
  is visible which corresponds to the minor groove facing
  towards RepA.
  Such a large amount of sequence conservation
  in the minor groove
  ($> 1$ bit) is not possible with B-form DNA,
  so the base must be distorted.
  This figure
  was
  the cover of \emph{Nucleic Acids Research}
  Volume 29, Number 23,
  December 1, 2001
  \cite{Schneider.baseflip.2001}.
  }
  \label{fig.baseflipcover}
  \end{wrapfigure}
  }
  

  More information may be found in: Guide to LATEX: Document Preparation for Beginners and Advanced Users by Helmut Kopka, Patrick W. Daly. Buy it!!