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.
- 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.
- 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.
- See also Increasing the Resolution of a Linux VirtualBox Guest.
- Using VMware instead of VirtualBox is not recommended, as ARB is known to die in VMware with the error message:
/home/username/arb/bin/arb_ntree: 1: Syntax error: Unterminated quoted string
- 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
- 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
- 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.
- 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
- Now, we need to create a few environmental variables so the computer (and ARB) know where to find ARB.
- Type this command:
sudo gedit /etc/bash.bashrc
- Add the following lines:
export ARBHOME=$HOME/arb alias arb='$ARBHOME/SH/arb'
- Save the file and exit gedit.
- Close/reopen your terminal windows.
- Type this command:
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.