mylinuxnotes

Wednesday 20090617

Installing ARB in Ubuntu Hardy LTS

Filed under: ARB, bioinformatics, howto, install, ubuntu — Tags: — jeff @ 9:47 pm

How to install ARB on Ubuntu Hardy LTS.  These are my notes of what worked on my system, and depending on what you already have installed, you may have additional requirements.  (Please feel free to make note of your experience in the comments, if you’d like to share!) This is a modified copy from my previous post for installing in Feisty Fawn.

Make sure you have the prerequisite packages installed:

  • transfig
  • xfig
  • xviewg
  • gv
  • libmotif3

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.

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1 Comment »

  1. I am using the latest ARB 5.1. I cannot start the server; instead I get this message:

    All species contain data in alignment ‘ali_16s’.
    PT_SERVER: Error while opening file /usr/arb/lib/pts/user1.arb.pt
    AISC_ERROR: CONNECTION PROBLEMS
    Waiting for server ‘ARB_PT_SERVER3′ to come up (10 seconds left)

    Any idea?

    Comment by Tandi — Tuesday 20091110 @ 12:57 pm


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