Installing Zotero standalone on Ubuntu 11.10

Zotero is an open source reference manager, produced by the Roy Rosenzweig Center for History and New Media.  To say ‘reference manager’ understates what it is capable of: you can use it to organize your reading, collaborate with others, and produce bibliographies in a matter of seconds.

Having started off as a Firefox plug-in, it has recently released a beta of a stand-alone application. More versatile than the browser-based version, it is however a little more tricky to install on Linux. (On OS X it installs via the usual click, drag and drop.) Hence this post. These instructions are based on Ubuntu 11.10, with the Unity desktop, but they should work for any variant. Certainly it works for my preferred flavour, Xubuntu.

Warning: this is beta software! Warning 2: these instructions come with no guarantee of success!

1: Download the Zotero standalone tarball. For a 32bit chip, you’ll want the x86 version, for a 64bit get the x86_64. If you don’t know what type of system you have, open a terminal and type:

uname -m

You’ll get something like i686 if you are running a 32 bit system, and x86_64 if you have a 64 bit system. Note that you may be able to run the 32 bit version of Zotero on a 64 bit system, and that even if you have a 64 bit chip, your version of linux might be 32 bit.

2: Unzip it. You’ll now have a folder called Zotero_linux, appended with -i686 for the 32-bit version, and -x86_64 for the 64bit. [Update 1, 16/7/12: I missed a line here: Open the folder and locate the executable file, named ‘zotero.’] Right click on it, choose ‘properties’ from the menu, and then the permissions tab, and tick the ‘Program’ box to allow it to run as a program.

3: As it stands, Zotero will work. But having the package in your home directory is a bit messy, and means it isn’t available for all users of the computer. So to be both neat and useful, open a terminal and type

sudo mv ~/Downloads/Zotero_linux-i686/ /opt

This will move Zotero to your /opt directory. Note that because this is Ubuntu, the command has to be run with sudo. For many other linux distros, you’ll have to log in as root.

4: So far so good, and so easy. The next step is to get the system to recognize that it has been installed. To do this you have to make a .desktop file in usr/share/applications. Copy and paste the following text into a file called zotero.desktop:

#!/usr/bin/env xdg-open
[Desktop Entry]
GenericName=Bibliography Manager
Exec= /opt/Zotero_linux-i686/zotero %f

Then send it to usr/share/applications, where most of the .desktop files reside:

sudo mv zotero.desktop /usr/share/applications

5: And finally, find and run it. Go to the ‘dash’ in the dock – or Application Finder, under Accessories in the Xubuntu menu – search for zotero, and it should show up under applications. Click and all being well, Zotero will start up. If you want to keep it in the dock, right-click the icon and tick the option to keep it there.

Uninstalling: To remove Zotero, open a terminal and type: sudo rm -r /opt/Zotero_linux-[version] and sudo rm /usr/share/applications/zotero.desktop. The users own files are in the hidden folder ~/.zotero.

[Update 1, 16/7/12: Missing line regarding permissions in step 2 inserted.]

[Update 2, 16/7/12: These instructions work for the latest Xubuntu release, 12.04; so presumably they will also work for Ubuntu 12.04.]

[Update 3, 16/7/12: Zotero is currently at version no. 3.0.8. Automatic updating from within the linux port doesn’t work; to upgrade just install the new version of the old, following steps 1 – 3 above.]

[Update 4, 10/7/14: Zotero is no longer beta, is at version for Linux, and automatic upgrading now works. Download link above changed. Further, there is now an Ubuntu PPA for Zotero on Launchpad.]

Further support for Zotero can be found on their documentation pages and forums. This post is copyright under the CC BY license. Use to your heart’s content, but please acknowledge me!

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51 Responses to Installing Zotero standalone on Ubuntu 11.10

  1. Jeremy says:

    Thanks for the helpful guide!

    I thought it might be helpful to add that – if you installed the 64 bit version – the paths to the icon and executable will be:

    Exec= /opt/Zotero_linux-x86_64/zotero %f


  2. Andrew says:

    Thanks – this is very helpful and worked perfectly, except there is an error in the zotero.desktop file in the Icon line. It should read “Icon=/opt/Zotero_linux-i686/chrome/icons/default/default48.png”. What you have above will not link to the zotero icon and there will be a question mark in the launcher instead. But other than that, this is great – thanks again!!

  3. johnl says:

    Thanks for catching this – I’ve corrected the post.

  4. Steven says:


    Thanks for the great post. Following the directions has very easily allowed me to install Zotero standalone! Please keep up the good work!


  5. Pingback: Installing Zotero | thegodfather2

  6. John says:

    Thanks so much for this. Makes so much sense. Much appreciated.

    All the best. John

  7. Michael says:

    This is great–thanks for the help.
    FWIW, I ran into a problem with Step 2, as I was unable to “tick the ‘Program’ box to allow it to run as a program.” The box just wouldn’t tick. I did some searching and it seems like in some similar cases it worked to move the folder to the desktop first. Didn’t help me, no matter where I put it. I was able to go into the folder and change zotero.jar (I think) and it ran fine after that (though I haven’t done much with it except play with duplicates!)

  8. Freddy Mendoza says:

    A perfect guide!!!

    Muchas Gracias

  9. ben says:

    Happy Australia Day!

    Thanks for the simple guide, much appreciated. Good to know how easy it is to create those .desktop files.

  10. Jay says:

    Perfect! Thanks so very much. Thanks also to Michael for the 64-bit info.

  11. Jake says:

    I am new to Ubuntu and having a spot of bother with step 4. Do you have to create the document ‘zotero.desktop’? If so then I understand you have to paste the text in once created but I don’t know how to create it in the first place.

  12. johnl says:

    Hi Jake,
    Just open Gedit, the default text editor on Ubuntu, copy and paste the highlighted text into it, and then save it with the name ‘zotero.desktop’

  13. Adam says:

    Thanks for this — very helpful!
    I noticed as well that I didn’t need to make the “Zotero_linux” directory executable as a program (in step 2), but I did make “/Zotero_linux-x86_64/zotero” executable in that way (or it was already set up that way, I installed a while back). Everything else worked perfectly. Thanks.

  14. Moritz says:

    Thanks a lot for this thorough guide! It works perfect for me except for one thing:

    When I start Zotero, keep it in the panel, then start it through a click on the icon in the panel, I end up with two icons in the panel. When I do this again, I have three icons in the panel, and so on.

    Does anyone maybe have an idea what is going wrong?

  15. Christof says:

    Hi there, thanks for this great guide which makes the installation so much nicer! Allow me to point out that in order for the icon to show up correctly in the launcher, the path in the zotero.desktop file should be the one indicated by Andrew, i.e. with a capital “Z” in “Zotero”.

  16. johnl says:

    Ah, thanks for catching this. Now fixed.

  17. chilloutmo says:


    Thanks very much for the how to, worked well. But I experience the same problem as Moritz. When keep zotero in the launcher and click on it, I have two icons, next time three, and so on. Any idea on what could help?


  18. johnl says:

    Not sure what is happening; at a guess it sounds like you have more than one instance of Zotero running. Could you open System monitor and see if that is the case?

  19. chilloutmo says:

    No, there is never more than one instance of Zotero running, even when there are several icons in the launcher. It’s not the end of the world if I don’t have it in the launcher, it works fine from the dash, but it’s still intriguing why it doesn’t work correctly…

  20. Thanks for your help! I might write a post on Zotero and how to install it in my blog but be sure I will give you all due recognition

  21. johnl says:

    Happy to help, and please feel free to use anything you require from this post!

  22. Saranga Sumathipala says:

    Many thanks. Works like gold. I’ve been dependent on commercial apps. Now open source is the champion of the free world.

  23. bob says:

    nice. thanks. i had trouble getting zotero standalone to work before i found your writeup, so the first time i ran it was by using sudo. that made my .zotero profile under root, so it wouldn’t load my profile after following your instructions. chown ~/.zotero back to your user fixed the problem. Just FYI for others.

  24. Kamal says:

    Hi there,

    I am a new user of ubuntu. I face some problem in installing the program. After downloading, the file is saved as “Zotero-3.0.7_linux-i686.tar.bz2” in the downloads. I right clicked and in permissions tab I ticked the box “Allow executing file as program”. What should I do next since there is only an option to close the dialogue box. I don’t have an idea.

    In case if I double click on the above said folder , I see a folder “Zotero_linux-i686”. Here if I right click I couldn’t see the properties option. Please help me to install the program.


  25. johnl says:

    Once you have ticked the ‘allow executing file as program’, you can just close the dialogue box. It should remember the setting.

  26. Worked great and in an older gnome interface (can’t get the hang of unity). Thanks!

  27. Pingback: » Installing Zotero in Ubuntu the dpod blog

  28. toml says:

    Neat guide, thanks for putting online. It works fine, but after I reboot the icon is not present in the menu listing. However, re-opening and saving the file in sudo then immediately restores it to the menu list. Any idea what’s causing this?

  29. winny says:

    i have ubuntu 12.10
    follow all of your steps.
    when I click the icon, nothing happened.

    why was that ? how do I check ?


  30. Karoliina says:

    Thank you so much!!
    Winny, I had the same problem until I realized that since I’m running a 64bit system, I installed the tarball for 64bit system but followed the instructions (for 32bit system) too closely and ended up having the same problem. Then I read Jeremy’s comment again and realized that that was my problem. I changed the two lines in zotero.desktop file and now it’s running smoothly.

  31. Caio says:

    Just adding my thanks to those already here. You’ve saved me a lot of trouble. Best!

  32. Luis says:

    Nice tutorial, works perfect, maybe i’ll be worth it to mention that if you are running 64 bit your folder is different and the .desktop file is different, it took me a minute, but is good to mention. Thanks a lot

  33. Corsair says:

    Worked great for me after I changed the pathway in the .desktop file (Zotero_linux-x86_64 instead of Zotero_linux-i686) to match with the name of the file I downloaded.
    As mentionned above it might be interesting to add it in the tuto!
    Thank you anyway 🙂

  34. chtfn says:

    Hi johnl (or anterotesis)!

    I was wondering: on your post on Zotero’s forum, you talk about “global menu”. Does your Zotero standalone actually integrate its menu in the top panel in Ubuntu? Or did you mean that you are able to find the app in the dash and that you can pin it to the Unity launcher?

    I would love to figure out a way to integrate Zotero with the global menu. Any clues?


  35. johnl says:

    I mean the Unity launcher, rather than the top panel application menu. Am currently using Zotero on Xubuntu, so can’t investigate this right now, but will investigate the next time I install Ubuntu.

  36. chtfn says:

    Cool, thanks for explaining! Cheers 🙂

  37. Lenartalot says:

    Thank you.

  38. Maria says:

    Just used this and it worked perfectly. Thanks!

  39. Pingback: Gérer sa bibliographie avec Zotero | Redoc Paris-Est

  40. Usodimare says:

    Thank you John! Your instructions work well even with Lubuntu 12.10 and Zotero 4.0 Beta.

  41. waonx says:

    Thanks! It worked great in Linux Mint 14

  42. dlahr says:

    Thanks so much, I needed to figure out how put something in my applications path AND am getting more and more into Zotero (very cool tool).


  43. Lisa Munro says:

    Works perfectly on Linux Mint 14…thanks for taking the pain out of the installation!

  44. Ben Barwick says:

    Awesome! On Ubuntu 13.04 kernel 3.8.0-19 64 bit

  45. Pingback: How to Install Zotero Standalone on Ubuntu 12.04 LTS | Adrian Dobre

  46. Afrothetics says:

    These instructions still work perfectly in version 4.0.23 and should be provided as a link at as well for new users.

  47. Afrothetics says:

    I should add that these instructions work on the recent versions of Linux Mint, also.

  48. Karibe says:

    Thank you, was helpful especially the tip of moving to /opt 😛 and the .desktop stuff was on point for copy-paste

  49. Rendon says:

    Hello! First, thanks for such a clear guide. I have followed these instructions and see Zotero in the Applications Menu. However, I click and nothing happens! Any obvious mistakes I may be making? Thanks

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