Dan's Blog A cheat sheet for random challenges

12Dec/1024

Basic ARB Installation Instructions

ARB is an excellent software suite for phylogenetic analysis of 16S rRNA and other biological sequences.

Installing and setting it up however can sometimes be problematic. I've installed this software many times and will explain here how I've gotten it working when ARB's installation manual wasn't enough.

This walkthrough was put together immediately after I installed a fresh version of Ubuntu 10.10 (ubuntu-10.10-desktop-amd64.iso) into a VirtualBox virtual machine.

Basic Installation

  1. Start with Ubuntu! Grab the 64-bit version of release 10.04 (later releases might also work). This is the operating system that ARB was developed on and for. Starting with it will make your life much much easier.


  2. Can't install Ubuntu? Install VirtualBox, then install Ubuntu into a virtual machine. You can keep your existing Windows/Mac/etc just as it is while making ARB nice and comfy.
  3. Now that you've got a 64-bit Ubuntu environment, download and extract the tarball thusly:
    cd ~
    mkdir arb
    cd arb
    wget http://download.arb-home.de/build/latest/arb.64.ubuntu.tgz
    tar -zxvf arb.64.ubuntu.tgz
    


  4. The latest ARB release as of this writing (ARB 5.1) requires a modification to its directory structure. If you omit this step, ARB will give you the error message "/home/username/arb/lib/pts doesn't exist" when building a pt server. The following commands replace the ~/arb/lib/pts file with a folder of the same name, and will not hurt a correctly structured directory.
    rm -f ~/arb/lib/pts
    mkdir ~/arb/lib/pts
    


  5. There is a second known error in the current version of ARB: in ~/arb/lib/arb_tcp.dat on line number 55, "-fstart" should be "-fstart=1". Make this change via gedit (displays your current line number in the lower-right corner). Save and exit when you're finished. Without this fix, you'll receive an ambiguous error message when you try to automatically rename imported sequences, or during any other event which requires a name server.
    gedit ~/arb/lib/arb_tcp.dat
    


  6. To work, ARB will need a bunch of extra libraries. Install them using the command below. Note: the following is all one line.
    sudo apt-get install libmotif3 libpng3 xloadimage gnuplot gv xfig libglew1.5
    


  7. Now, we need to create a few environmental variables so the computer (and ARB) know where to find ARB.
    1. Type this command:
      sudo gedit /etc/bash.bashrc
      


    2. Add the following lines:
      export ARBHOME=$HOME/arb
      alias arb='$ARBHOME/SH/arb'
      


    3. Save the file and exit gedit.

    4. Close/reopen your terminal windows.

You should now have a functional ARB installation. Just type "arb" to launch the program. This setup will work fine if you only have one ARB user, or all the ARB users are okay with sharing a single ARB installation.

Do not run multiple instances of ARB at the same time. The configuration file for ARB (~/arb/lib/arb_tcp.dat) has hard-coded port numbers. This means if more than one ARB is launched at the same time, they will potentially conflict and crash.

If you want to configure an environment that supports concurrent ARB users, please see part two of this tutorial - Modifying an ARB Installation for Concurrent Users.

Please leave me a comment below if these instructions did not give you a working installation of ARB on Ubuntu. Be sure to include any error messages produced by ARB in message boxes or emitted to the terminal. I'll try to find a fix and update these instructions accordingly.

Comments (24) Trackbacks (0)
  1. I was trying to install arb in ubuntu using the VM player and getting this error message. I was wondering if you had any suggestions.
    Thanks,
    Shreya

    shreya@r95oertherd:~$ arb
    Using ARBHOME=’/home/shreya/arb’
    Please wait while the program ARB is starting …..
    /home/shreya/arb/bin/arb_ntree: 1: Syntax error: Unterminated quoted string
    shreya@r95oertherd:~$ ARB done

  2. Mr. Dan,
    I am with Missouri S&T and I am working with a grad student who is needing ARB.
    Your tutorial is much simpler then the developers original doc. Thank you for that.

    However, I have tried this on 6 attempts using various virtual Ubuntu builds and now a native install and I keep getting this error:

    /home/sg7vc/arb/bin/arb_ntree: 1: Syntax error: Unterminated quoted string

    Is this something you have seen before?
    I am not sure what causing it.

    We have tried:
    Ubuntu 9.10 x64 in VM
    Ubuntu 9.10 x86 in VM
    Linux Mint 10 x64 in VM
    Ubuntu 10.10 x64 in VM
    RHEL5 x64 in VM
    Ubuntu 9.10 x86 native hardware

    • Hi Randy (and Shreya above),

      From our personal correspondence, it seems that VMware may be the cause of this error message, since you were able to get ARB running in VirtualBox.

      Thanks for the heads-up on this issue!
      -Dan

  3. Hello!

    I´ve tried this guide and ARB works fine, exept there are still some problems with the name server. For instance when merging two databases, its not possible to autorename the species in DB1. How can I add a new name-server?

    Best wishes,
    Fabian Faßhauer

    • Hi Fabian,

      I don’t know much about name servers. But, there has been a bit of discussion lately on the arb_users mailing list about this issue. After registering, you can read up on it: http://tech.groups.yahoo.com/group/arb_users/

      I believe you can add a new name server by editing the arb_tcp.dat file. Look for lines with “ARB_NAME_SERVER”. I’ve never added one before myself though, so good luck!

  4. Hi!
    A great guide for a noob like me! But I’m also getting the error message that Ron and Shreya are getting.
    …arb/bin/arb_ntree: 1: Syntax error: Unterminated quoted string.

    Odd. I’m running Lucid Lynx.

  5. Hi,

    I am running ARB on Ubuntu 10.10 through VirtualBox 4.04 on a Windows 7 platform.
    I was having similar problems as Shreya and Randy. I performed all the steps listed above while skipping step 5. This seemed to have resolved the “arb_ntree: 1: Syntax error: Unterminated quoted string” error. For now things seem to be running smoothly, however I am not sure if I will run into issues while renaming imported sequences.

    Thanks.

  6. Hey… Thanks for the information!
    I have Windows xp and I already installed the Ubuntu. When I am trying to open it up, (switch it on), than the black screen appears, and the message on it that says
    WIN7 host, FATAL: No bootable medium found! System halted. I tried to find the solution on line, but it is hard for me to understand the technical language… could you explain please what to do in layman terms?
    Thanks a lot!

  7. I have just updated my operating system (in VirtualBox) from Ubuntu 10.10 to 11.04 however when I attempt to run arb I receive the error message “arb_ntree: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory” any ideas?

    Thanks

    Michael

  8. Michael,

    Try: sudo ln -s /usr/lib/libXm.so.4.0.3 /usr/lib/libXm.so.3

    This worked for me.

  9. I am using Ubuntu 11.04 and have followed your instructions (well i hope) and have been having a problem. ARB open perfectly fine, but when I attempt to perform an action such as using arb aligner or tree builder I get these types of responses on terminal without any action
    [Action: 'arb_edit4 -c default_configuration &'] or [Action: 'arb_dist &'].

    Do you have any insight on my problem?

  10. Thanks, Dan! I just installed ARB 5.3 in Ubuntu 10.04 LTS (Lucid Lynx) via the Ubuntu WUBI installer for running with my Windows 7. Fortunately ARB now seems much easier to install than when you wrote this, but it did not correctly edit my bash.bashrc config file so I was very glad to find your post.

    For those of you reading this looking for a up-to-date was to install ARB I’ll let you know what I learned the past week wracking my brain to make it work:
    1. Use Ubuntu 10.10 or earlier release. ARB 5.3 (current Feb 2012) requires libmotif3 which is not available in Ubuntu releases beyond 10.10, instead they use libmotif4
    2. If you’re installing on a machine already running Windows, using Ubuntu’s WUBI tool makes it all much easier. And will make it much easier to uninstall Ubuntu later if you want to. If you want to install a version of Ubuntu older than the current release with WUBI you’ll need to download your desired release tar file of Ubuntu AS WELL AS the release-specific version of WUBI.
    3. When installing ARB 5.3 be sure to read over the ARB files: readme, install, and ubuntu. These all have useful info.

    As mentioned above, my new install of ARB is working well and I only had to fix the bash reference following step 7 above (and substituting the directory that I had installed ARB into for Dan’s “$HOME/arb”. That said, I have just started playing around in ARB so I can’t comment on deeper issues running with the setup I’ve described. Will return and do so if I hit any.

  11. Thanks for your instructions.

    I am trying to install ARB on unbuntu 11.10 but am getting the following error
    arb_ntree: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory

    I run the following command sudo ln -s /usr/lib/libXm.so.4.0.3 /usr/lib/libXm.so.3 but am still getting the same error.

    Do you have any suggestions.

  12. @Nate:
    My understanding is that ARB cannot run in Ubuntu 11+ because those versions use the libmotif 4 library and ARB needs libmotif 3. Thus you can only run ARB in Ubuntu 10 or earlier. I don’t think it’s possible to get Ubuntu 11 to run with libmotif 3 (and you cannot have both 3 and 4 running simultaneously). A couple months ago a spent a week just getting Ubuntu and ARB working on my comp – see my above comment for the other stuff I learned through that.

  13. I installed arb using ubuntu (latest version 11.0) and the instructions above but I am getting the following error. Can someone help me with that?

    “arb_ntree: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory”

    • I ran into that problem as well. See my comments above on how to avoid that issue. Short story, you can’t use ubuntu 11.

  14. Your tutorial is wonderfl for beginners like me. I installed arb successfully but the problem is as follows
    I downloaded “SSURef_108_SILVA_09_09_11_opt.arb” database now when I have saved this file on desktop and when I open this using arb it results in automatic shut down of arb leaving this message in the terminal

    /home/shamsalig/arb/SH/arb: line 148: 3639 Killed arb_ntree $args

    Any Idea? why this is happening?

    • I have got exactly the same “error message”. I can open the demo.arb database when I tried the “SSURef_108_SILVA_09_09_11_opt.arb” database, it failed. Does anybody has an idea how to solve this??

  15. Hi
    I’m using VirtualBox and Ubuntu 10.04. I’ve installed the 64 bit of arb.
    When I run arb I get this message:

    Please wait while the program ARB is starting …..
    hts223@hts223-desktop:/$ usr/arb/SH/arb: line 146: usr/arb/bin/arb_ntree: cannot execute binary file
    ARB done

    Could you please help me out here ?

  16. As posted by Brian Perkins, above:

    Try: sudo ln -s /usr/lib/libXm.so.4.0.3 /usr/lib/libXm.so.3

    This seems to have me working in Ubuntu 12.04 LTS

  17. After initial download of ARB, building a PT-Server runs fine. However, after either 1) letting ARB sit idle overnight or 2) logging out, starting arb again, and trying to re-boot the PT-Server, i get a yellow error box with the following: tere is no data-base, not allowed to run ssh host pt_server, the permissions of $ARBHOME/lib.pts/ do not allow read access, the PT-Server host is not up, the tcp_id is already used by another program. As well, when I look at the terminal , i see errors saying; “Could not open socket on Server (1)” repeated over and over again. Any suggestions would be helpful. Thanks,

  18. Hi! I was following your instructions, but it seems that I cannot install ARB. I am using ubuntu, and as I work with terminal I follow all your instructions but when I close and open terminal again and type in arb, it does not recognize it.

  19. got all the way to the end and got this error message before the last command
    (gedit:8202): GLib-GIO-WARNING **: Missing callback called fullpath = /root/.local/share/recently-used.xbel


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