mylinuxnotes

Tuesday 20070925

howto: install ARB in Ubuntu Feisty

Filed under: ARB, bioinformatics, howto — jeff @ 3:48 pm

Make sure you have the prerequisites (most notably, in Feisty, the libstdc++2.10-glibc2.2 package, which I had to do some digging to figure out):

  • transfig
  • xfig
  • xviewg
  • gv
  • libstdc++2.10-glibc2.2 (in the universe repository)

Download the latest ARB for linux at www.arb-home.de.  The download directory contains three files; you need to put all of them in the same place: arb_install.sh, arb.tgz and zcat. No need to untar anything.

In the directory where you put these downloads,

$ sudo sh arb_install.sh

The script asks a bunch of installation questions, and it’s pretty self-explanatory about what it’s asking, so go nuts.  I used all the defaults for a stand-alone computer, except I used /opt/arb as the install directory instead of /usr/arb.

When the script exits, it mentions editing something in /etc (but it doesn’t say what).  In Feisty, you need to add the following lines to the /etc/bash.bashrc file (assuming you used /opt/arb as the installation directory like me–otherwise, you may have to replace “opt” below with “usr”):

ARBHOME=/opt/arb;export ARBHOME
LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
PATH=${ARBHOME}/bin:${PATH}
export PATH
alias arb=/opt/arb/bin/arb
echo “This shell is ARB-enabled.”  #Not necessary.  Just for fun.

It now seems to work!  You can delete the installation files.  Or, you can change your current installation by running arb_install.sh again.

15 Comments »

  1. Hello there! I got Arb running on Ubuntu but the problem is the PT server. When I want to update server there comes the message :”Tried to connect to session manager, Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed” in the administration terminal. I tried a lot but don´t know what to do….

    Comment by arborer — Saturday 2007106 @ 3:38 pm

  2. Hello! Are you running the PT server on the local machine, or connecting to a remote server? If you’re running everything on one local computer, I’m not sure what to suggest, because it just worked for me using the default installation. (During the installation script I selected the options to set up the PT server on the local machine, and to allow all users permission to update the database). If the server is on the local machine, I would guess that your error message might indicate you don’t have permission to write to the database file or folder.

    It sounds like you might be trying to connect to a remote PT server, however, in which case I’m sorry but I don’t have any experience trying to do that.

    I don’t know what your experience level is with using ARB, but I found this tutorial

    http://www.mm.helsinki.fi/users/GJURGENS/Arb/ARB_tutorial.htm#GETTING_STARTED

    to be very helpful. (I’m a beginner with ARB.) Section 3.6, “About the PT_Server,” begins to describe making updates to the server, and all of the examples worked for me. Good luck getting it to work for you!

    Comment by jeff — Saturday 2007106 @ 5:25 pm

  3. I think I figured out what was the problem with the Pt Server, the ssh daemon was not up. The only problem is that I cannot find the library libstdc++2.10-glibc2.2 you are refering to…

    Comment by arborer — Monday 20071015 @ 10:31 pm

  4. http://packages.ubuntu.com/feisty/libs/libstdc++2.10-glibc2.2

    libstdc++2.10-glibc2.2 is in the universe repository, but unfortunately it’s only available for i386 (no 64-architecture, bah!).

    If you have a 64, you may have to force the install to ignore architecture, and work around the problems that this creates. This reportedly works for libstdc++2.10-glibc2.2, according to these instructions:

    http://ubuntuforums.org/showthread.php?t=145506

    Good luck!

    Comment by jeff — Tuesday 20071016 @ 11:39 am

  5. ARB ran for me after following your instruction except for one little problem so far. When I attempt to “Edit sequences” and “using marked species and tree”, I get the message “error while loading shared libraries: libGLEW.so.1.3: cannot open shared object file: No such file or directory”.
    Any thoughts on what I should do to solve this problem? Yes, I am fairly new to this.

    Comment by Dan — Friday 20080523 @ 2:51 pm

  6. I have a same message “error while loading shared libraries: libGLEW.so.1.3: cannot open shared object file: No such file or directory” on Ubuntu 8.04 LTS Desktop !!

    Comment by Roger — Monday 2008069 @ 1:58 pm

  7. Changing the symbolic link to solve the problem : sudo ln –s /usr/lib/libglew.so.1.5 /usr/lib/libglew.so.1.3

    Comment by Roger — Wednesday 20080611 @ 1:25 pm

  8. Great, thanks for sharing the fix! I haven’t tried ARB in Hardy yet…

    Comment by mylinuxnotes — Wednesday 20080611 @ 1:39 pm

  9. ps linux is case sensitive so you have to do…
    sudo ln –s /usr/lib/libGLEW.so.1.5 /usr/lib/libGLEW.so.1.3

    I also had to make another link…
    sudo ln -s /usr/lib/libpng12.so.0 /usr/lib/libpng.so.3

    Comment by rec — Friday 20080613 @ 9:00 pm

  10. Hi I had the same error and made the links but is still not working I am getting the same error again and i cant edit my aligments. Any suggestion?

    Comment by juan — Tuesday 2008071 @ 9:53 pm

  11. Sorry my error is different I had this error while trying to edit a sequence:error while loading shared libraries: libpng.so.3: cannot open shared object file: No such file or directory
    so is no GLEW
    What can i do?

    Comment by Juan — Tuesday 2008071 @ 10:00 pm

  12. I also getting this error when i open the selected tree
    The path ‘/home/bartonlab/.arb_prop/inputMasks’ is invalid.
    Has it somethign to do?
    Tahnk you for your help

    Comment by Juan — Tuesday 2008071 @ 10:06 pm

  13. When I open pt_server and do fast alignment,arb makes error “sh: /sw/share/arb/bin/arb_pt_server: No such file or directory” in terminal window and make message “cannot contact pt_server” in ARB_EDIT4 window.
    Please any suggestion.

    Comment by Hideki Inaba — Monday 2008091 @ 2:19 am

  14. [...] howto, install, ubuntu — Tags: Hardy — jeff @ 9:47 pm Modified copy from my previous post for installing in Feisty Fawn.  As far as I know, this worked for [...]

    Pingback by Installing ARB in Ubuntu Hardy LTS « mylinuxnotes — Wednesday 20090617 @ 9:47 pm

  15. For those seeing “cannot contact pt server” have you built the pt database?
    Under the probe menu click on PT_SERVER Admin.
    Then click on the server template you want and click the Build Server button.

    Comment by laalaa99stl — Monday 2009076 @ 4:12 pm


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