How to Install Zotero Standalone on Ubuntu 12.04 LTS

After reviewing several reference management software (Wikipedia, WISC.edu, Imperial.ac.uk, Columbia.edu) I opted for Zotero. It’s simple to use, free, and open source. It has a 300 Mb limit with the possibility to buy extra space. Although 300 Mb doesn’t seem like a lot, it’s fine for the moment.

Zotero has a Firefox plugin that’s in constant connection with the server. You can also chose to have it installed locally, on your machine.

The following steps apply for a Zotero 4.0 standalone package on Ubuntu Studio 12.04 LTS, 64 bit.

1. Which package should I download?

Most of the time, zotero.org will propose a package that suits your system. If you’re not sure whether your computer runs on 32 or 64 bit chips, type this in the terminal window.

uname -m

2. Download

-> Go to https://www.zotero.org/download/ and download Zotero standalone with the browser extension of your choice.

-> extract the archive from its tar.bz2 compressed format

-> move the folder to your /opt directory, alongside other programs. You can do this in two ways

a) open a terminal window and type:

sudo mv ~/Downloads/Zotero_linux-x86_64/ /opt

This will move the Zotero extracted directory from your Downloads location to the /opt directory

b) open your Home folder -> press ALT+F2 -> *type gksudo nautilus -> click Run -> type your password -> OK

Navigate in the newly opened window to File System -> Opt

Paste here the Zotero folder you extracted in your Downloads location.

3. Make a .desktop file in usr/share/applications in order to make the system recognize that you have installed Zotero, and to be able to find it in your Applications Menu

-> open gedit or other text editor and type:

#!/usr/bin/env xdg-open
[Desktop Entry]
Type=Application
Name=Zotero
GenericName=Bibliography Manager
Icon=/opt/Zotero_linux-x86_64/chrome/icons/default/default48.png
Exec= /opt/Zotero_linux-x86_64/zotero %f
Categories=Office
Terminal=false

Be sure to change the Icon and Exec lines if you run on 32 bit

Icon=/opt/Zotero_linux-i686/chrome/icons/default/default48.png
Exec= /opt/Zotero_linux-i686/zotero %f

-> save the file as zotero.desktop somewhere on your computer and then paste it in usr/share/applications. Be sure to do this in the window of Step 2/b, that gives you root access.

Done.

I would like to reference http://anterotesis.com and his original post Installing Zotero standalone on Ubuntu 11.10. I used his steps and page comments to install version 4.0, changing somewhere along the way from terminal use to folder view.

* you might need to type kdesu konqueror or gksudo thunar if you have Kubuntu (KDE) or Xubuntu (XFCE) – read more here – http://www.psychocats.net/ubuntu/permissions

Change Okular Default Highlighter Color – for Linux Light Users

Update: Okular version 0.17 has configurable review tools.

Today I had enough of the yellow highlighter that’s default in Okular and I went about to change it. It was a bit tricky since I’m a light terminal user, and I wanted as much graphical interface as possible when dealing with changes in restricted areas of Linux.

Why do it? The yellow highlighter blends with the yellow color whenever I use CTRL+F to find a word in my research articles. It was annoying and I needed to change that.

After searching and reading, here’s the method that worked for me:

System: Ubuntu Studio 12.04 LTS

Okular: 0.14.3

Step 1: Know the color you want to switch to. You can do this in several ways:

a) Open a pdf with Okular and, using the Yellow Highlighter [4], highlight a text.

-> Right lick on the highlighted text and choose Properties.

-> Click on the actual color field next to where it says Color

-> Choose one of the colors that are available or create your own color, then copy the HTML code. In my case is #FFDCA8

OR

b) go to a site like http://www.computerhope.com/htmcolor.htm#03 and choose from one of the HTML colors there.

Step 2: Switch to Root

As you may know by now, when you’re using Linux (Ubuntu), you are a user without rights to modify critical system files. This is for your own protection and makes Linux very secure. But for this task you need root access – i.e. you need access to change one of these critical files.

Open your file browser (the Home button),

-> press ALT+F2

-> type gksudo nautilus (make sure you have Run in Terminal option checked). Click Run

– – > you might need to type kdesu konqueror or gksudo thunar if you have Kubuntu (KDE) or Xubuntu (XFCE) – read more here – http://www.psychocats.net/ubuntu/permissions

-> Type your password – OK

Step 3: Find the file and change the default color setting

Once you clicked OK after inserting the password, a new file explorer window opens.

->From the left menu click on File System

-> enter usr folder

-> enter share

-> enter kde4

-> enter apps

-> enter okular

-> right click on tools.xml and open it with your default text editor (like gedit)

-> search for Yellow Highlighter. It might look like this:

<tool id=”4″ name=”Yellow Highlighter” pixmap=”tool-highlighter-okular”>

-> change the default yellow color to the chosen color:

<engine type=”TextSelector” color=”#FFDCA8“>
<annotation type=”Highlight” color=”#FFDCA8

Important: Change only what’s inside quotation marks! For example, select the default #FFFF00 that represents color yellow and change it to the color code you chose in Step 1. In my case, as seen above, the new color is #FFDCA8.

-> save the file, close all programs, restart and voilà, job done!

Explaining these steps takes way longer than actually going though them. It’s very easy, as you’ll experience after the first try. You might have to do it every once in a while an Okular update arrives, and your tools.xml file will be overwritten by the updates.

Thanks to people on this forum, the solutions came from you guys – http://www.windowslinuxosx.com/q/answers-customise-okular-to-modify-highlight-tool-properties-584017.html

Hope this helps!

There are no images because that’s more of a self-imposed blog policy. Ask in the comments and I’ll do my best to describe things for you, or alt least guide you to someone who knows.

One Step Ahead: Ubuntu


The weekend that ends was dedicated to moving to a new system: Ubuntu Studio. Since computer time occupies sometimes +8 hours a day, I thought leaving the old XP was something to look into.

So I dove into this as a complete noob and came out dry. No dual boot, Linux all the way. What came as a great help where the more experienced users on Ubuntu Forums. Their answers came within hours and I received their support all the way.

I now run Ubuntu Studio and, to be honest, have no doubt I will keep this platform for the future.

Here are some links you might want to read if you consider switching:

http://www.youtube.com/watch?v=toO-WbLppl0 –  installing programs

http://www.techsupportalert.com/content/best-free-software-linux.htm – an updated software list of 10 pages, all free-ware

http://www.howtoforge.com/the-perfect-desktop-ubuntu-studio-11.10 – detailed installation guide for Ubuntu Studio

http://www.linuxbsdos.com/2011/05/04/manual-disk-partitioning-guide-for-ubuntu-11-04/ – manual disk partitioning guide

http://www.tuxfiles.org/linuxhelp/mounting.html – mounting drives in Ubuntu