Ubuntu for Research

Every so often it's time to upgrade to a newer release of your operating system of choice. If you are using linux and you are working in research, this might be an article just for you. Here are some instructions about the installation of Precise Pangolin 12.04, the ubuntu long-term support (LTS) release which has just come out and is to be supported until 2017.

I wrote two posts before, which were dedicated to installing software for research in ubuntu. This is an update for Ubuntu Precise Pangolin (12.04) a long-term support release. Installation should be extremely easy and basically a one-line command. You just have to love package managers.

If you want to install from scratch, download the new release from the ubuntu site. Otherwise, if you want to upgrade press alt-f2 (or open the terminal) and type
update-manager -d

Once you are done with the basic installation or upgrade, you are ready for more. This means more software repository sources, more software, more libraries. Below comes a basic list, Please feel free to suggest other programs in the comment section.

Connectivity

• The ssh server.
  
• Google Chromium (Chrome) - because it's very fast and now supports smart bookmarks (at least in linux versions)
  
• Dropbox - great for synchronizing files across computers and between users. Works with different operating systems.

Programming

• Powerful editors such as vim and emacs,
  
• gnu toolchain,
  
• gnu screen,
  
• subversion (svn), git,
  
• file converter from dos to unix (tofrodos),
  

Statistical tools

• GNU R,
  
• GNU octave,
  
• python with scipy,
  
• maxima,
  
• gnu scientific library.
  

Article writing and reference management

• texlive,
  
• many latex packages,
  
• Mendeley
  
• jabref and bibutils for converting to and from other reference formats.
  

Illustration

• graphviz,
  
• ImageMagick,
  
• gnuplot, pdfedit,
  
• inkscape,
  
• Scribus,
  
• gimp,
  
• plugins to play media contents, etc.
  

Others

• perl,
  
• java RE and SDK,
  
• blas
  
• boost libraries
  
• Zim is a note-taking/wiki application which is much faster than tomboy (presented some time ago on this blog).

Get a new and comprehensive ubuntu sources list from the ubuntu sources list generator. Choose your country, your ubuntu release (12.04) and all the software sources that you think could be useful. I chose for example the canonical partner, restricted, etc, and google linux repository among others. After pressing generate sources, you'll get a file that you should put as /etc/apt/sources.list (don't forget to backup the old one). On the same internet page, you find how to add the repository keys, which you should do before updating your sources (apt-get update).

For mendeley repositories do (you might want to check that 11.04 is still the latest release they officially provide packages for) sudo sh -c 'echo "deb http://www.mendeley.com/repositories/xUbuntu_11.04 /" >> /etc/apt/sources.list'

For the Adobe Reader repository do sudo apt-add-repository "deb http://archive.canonical.com/ $(lsb_release -sc) partner"

Download the latest package information. sudo apt-get update

I put all the software mentioned above and some more in a single command, so you have everything installed in one wash. No need to search or to sit around and try to fix things.

sudo apt-get install aptitude openssh-server build-essential gcc gcc-doc apt-file gsl-bin gsl-doc-pdf gsl-ref-html libgsl0-dev gsl-bin gsl-doc-pdf libgsl0-dbg libgsl0ldbl glibc-doc libblas-dev maxima maxima-share subversion subversion-tools git screen $(aptitude search R| grep -v ^i | awk '{print $2}' | grep ^r-) octave $(aptitude search texlive | grep -v ^i | awk '{print $2}') untex luatex perl fontforge context-nonfree context-doc-nonfree dvipng imagemagick graphviz gnuplot-x11 gnuplot-doc gnuplot libatlas3gf-base kdevelop kate kile vim-gtk vim vim-addon-manager vim-common vim-doc vim-latexsuite latex2html latex-beamer xpdf writer2latex jabref bibutils hevea hevea-doc wordnet cups-pdf djvulibre-bin djvulibre-plugin pdfedit inkscape scribus pdf2djvu pdf2svg pdftk python-gdbm ipython python3-dev python3-all python-scipy unrar tofrodos epiphany-browser epiphany-extensions scribes lyx claws-mail claws-mail-i18n claws-mail-doc claws-mail-tools libqt4-core libqt4-gui ubuntu-restricted-extras regionset soundconverter gxine libxine1-ffmpeg libstdc++5 libmms0 vim aptitude zim mendeleydesktop -y --force-yes icedtea-plugin sun-javadb-client gimp acroread wine colordiff moreutils

This will take a while...

For google chrome I posted instructions earlier. This time I followed instructions other instructions, which are as follows:

wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | sudo apt-key add -
sudo sh -c 'echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list'
apt-get install google-chrome-stable

Linux is an international effort translated into many languages. Depending on the "locale" you choose, your week may start with a Sunday, Saturday, or Monday. Say, you are not a Christian or Jew? You might want to change the first weekday in your calendar to Monday. Here's how.

What I found had difficulty to find at first was how to add applications to the launcher sidebar. Press the windows key, search for "Main Menu." You might have to install it first (you will get prompted). That's the application for editing the application menu that pops up on pressing the windows key and from this menu you can drag and drop items to the launcher sidebar.

You might want to see other of my articles for more tips, such as (for a short selection) smart bookmarks for faster web searches, how to synchronize web browser bookmarks on different work stations, personalize the vim editor, set up a revision control repository, and automatically synchronize data.
You can also see the UbuntuScience community page for some additional information.
Enjoy. Please leave a comment below for questions and suggestions.