Lyx is an open-source word processor built on top of LaTeX and Zotero is modern, open-source bibliography management package with “cloud” features. MetaUML is a system for creating UML diagrams in LaTeX (it’s frankly pretty painful to use but it does produce professional looking results). This post is where I keep my notes about installing and configuring LaTeX, Lyx and Zotero on my Ubuntu system at Imperial (where I do not have root access).

Installation

Install TeX Live 2011

First, download and install TeX Live 2011 (which includes LaTeX). Ubuntu 11.04 ships with TeX Live 2009 which lacks several features I need (specifically for handling graphics and graphs).

  • Download and unpack the [TeX Live installer](http://www.tug.org/texlive/acquire-netinstall.html). Beware: a full installation uses almost 3GBytes of disk space and takes a while to download and install.
  • If, like me, you're installing on a university-supplied Ubuntu machine to which you do not have root access then change the `TEXDIR` install directory by pressing `D` on the first screen of the TeX Live installation program to a directory to which you have write permissions. I use `/data/usr/local/texlive/2011` as my `TEXDIR` on my Imperial machine.
  • If you installed to a non-standard directory then you need to add that directory to your path. If you're using the bash shell then add `export PATH="$PATH:/install/directory"` to `~/.profile`. If you're using csh then also add `setenv PATH "$PATH:/install/directory"` to your `~/.cshrc`. For example, I use csh so I add `setenv PATH "$PATH:/data/usr/local/texlive/2011/bin/x86_64-linux"` to my `~/.cshrc` AND I also add `export PATH=$PATH:/data/usr/local/texlive/2011/bin/x86_64-linux` to my `~/.profile` file. If I modify `~/.cshrc` only then starting Lyx using the `ALT-F2` does not load with the correct path settings (the path in which I installed TeX Live 2011 and the path with the latest version of Lyx must come before the other path variables).\ #### Install GNU aspell If you have root permissions then just do `sudo apt-get install libaspell-dev`. If you do not have root permissions then: 1. Download source from <http://aspell.net/> 2. `./configure --prefix=/homes/dk3810/binaries && make -j9 && make install` #### Install Lyx 2.0.2 Now download and install the latest version of Lyx. 1. I have to install the binaries to a directory within my home directory because I do not have write access to /usr/bin so I run:`./configure --prefix=/homes/dk3810/binaries --with-extra-prefix=/homes/dk3810/binaries` 2. `make -j8` (replace "8" with the number of CPU cores available) 3. `make install` 4. If you installed in a non-standard directory then add that directory to your path. #### Install Zotero Download and install from [Zotero's download page](http://www.zotero.org/download/). I'm using 3.0 beta. #### Install MetaUML (after installing TeXlive 2011)\ In the install file, change the directory `TEXMF_HOME=/usr/share/texmf` to `/usr/share/texmf-texlive` (or whatever your TeX Live install directory is). ### Configuration #### Lyx configuration
    • Document > Settings: - Bibliography - Processor: bibtex8 (see Lyx manual sec 6.5) - PDF Properties - Enable “Use hyperref support” - Add a title and Author - In the “Hyperlinks” tab: - check “no frames around links” - check “color links” - enter `urlcolor=BlueViolet, citecolor=CadetBlue,linkcolor=black` into Additional Options - If using Document Class “book (KOMA-Script) then add `,usenames,dvipsnames` (with the leading comma) to “Document Class > Class options: custom” else add `\usepackage[usenames,dvipsnames]{color}` to LateX Preamble. See LaTeX WikiBook for more info on [hyperlinks](http://en.wikibooks.org/wiki/LaTeX/Hyperlinks) and [colours](http://en.wikibooks.org/wiki/LaTeX/Colors). - Listings > add `commentstyle={\color{blue}}` (or DarkOrchid) into the bottom box - Page Layout > A4 - Language - English UK - Encoding > “Unicode (utf8)” - Output > Default Output Format > PDF (pdflatex)
    • Tools > Preferences:
      • Output > Default Paper Size A4
      • Output > LaTeX > Uncheck “User LaTeX font encoding”
      • Editing > Shortcuts:
        • - Change bind file to emacs - Search for "view". Modify `buffer-view ps`. Delete the `ps` so the command is `buffer-view` and change the key binding to `Ctrl+Shift+X C`. - Search for "update". Modify `buffer-update ps`. Delete the `ps` so the command is `buffer-update` and change the key binding to `Ctrl+X C`. - Search for "buffer-write" (the command to save). Change keybinding to `Ctrl+X S`
    • Tell Lyx to pass the `-shell-escape` parameter to `pdflatex`. Go to Tools > Preferences > File Handling. Select "LaTeX (pdflatex) -> PDF (pdflatex)". Modify the "Converted:" field so it reads: `pdflatex -shell-escape $$i` . Click "Modify" and "Save". [this forum thread](http://tex.stackexchange.com/questions/16366/lyx-how-to-add-command-line-option-flag-for-latex-compiling) gives more details.
    LaTeX preamble:\ ` \usepackage{a4wide} \usepackage{graphicx} \usepackage{epstopdf} \usepackage[left=2.5cm,right=2cm,top=2cm,bottom=2cm]{geometry} % for dot2tex \usepackage{dot2texi} \usepackage{tikz} \usetikzlibrary{shapes,arrows} \usepackage[margin=10pt,font=small,labelfont=bf]{caption} \usepackage{textcomp} % For MetaUML: % The following is needed in order to make the code compatible % with both latex /dvips and pdflatex. \DeclareGraphicsRule{*}{mps}{*}{}`{language="latex"} #### Zotero configuration Preferences > Export > check “display character encoding on export” and select “UTF8” in the drop -down list. #### To enable URLs in references Download and install [urlbst](http://purl.org/nxg/dist/urlbst). Then: ` cp urlbst ~/binaries/bin cp *.bst /data/usr/local/texlive/texmf-local/bibtex/bst/local/ texhash`{language="bash"} (you'll have to use the correct directories for your setup). #### To stop duplicated URLs in bibliography Edit `/home/USER/.mozilla/firefox/HEX.default/zotero/translators/BibTeX.js`\ Comment out this code around line 2099: if(item.itemType == "webpage") {\ writeField("howpublished", item.url);\ } #### To change the colour of the links (not requried if using Lyx) ` \usepackage{hyperref} % required to get URLs into references \hypersetup{citecolor=blue,urlcolor=blue}`{language="latex"} <http://wiki.lyx.org/BibTeX/Tips> ### Use #### Bibliography 1. Export your bibliography from Zotero with Actions > Export Library > Format=BibTeX (do not export files). Save to file 2. In Lyx: Insert > List/TOC > BibTeX Bibliography. Press "Add..." and then "Browse" and select your .bib database file. 3. Now add individual references to your text with Insert > Citation.