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[last updated, Feb, 2012] | Fink | ARB home | GreenGenes | SILVA |

INTRO: This page is provided so that Mac users can install the phylogenetic database program called ARB. I have been running ARB on various mac computers since 2002 and it has been a wonderful and extremely useful tool for my research (microbial diversity in salt lakes). The german programmers keep on putting more exciting features into it, so it can be an incredibly powerful environment for bioinformatic analyses. The target plaftorm for ARB is linux, but this is a form of the unix operating system, like OS X, and the ARB source has been progressively revised so that compilation on OS X is now very easy. I used to use the Fink packaging system in earlier versions of OS X, but in 2009 Matt Cottrell modifie all the necessary dependent programs needed to install a 64-bit version of ARB, and he used macports. The installation works very smoothly but newcomers to unix need to do a bit of homework first. While he states it works for both Leopard (10.5) and for snow leopard (OS X 10.6), I have only installed it under 10.6. - and it works well.

To install ARB, you will need some knowledge of the unix operating system- not a lot, but a rudimentary grounding. Buy a book, look up web tutorials, anything. You need to be able to do simple things like know your way around directories, copy (cp) and edit files (e.g. pico editor), change privileges (chmod), have superuser (sudo) status, know about paths, listing (ls) directories and editing 'invisible' files (like .profile). Get familiar with the Terminal and X11 applications (Utilities folder). Having a unix person around can really help here.

10.7 - LION

I have been avoiding Lion because I have ARB working well on 10.6 and there seems little reason for me to change. At the same time I have noticed a couple of complaints voiced on the ARB discussion forum about setting up ARB on Lion. As far as I see, the instructions for Snow Leopard are valid for 10.7 EXCEPT for the following important issue (noted on the ARB discussion list, Feb 2012). There is a problem with the version of Xcode tools from the Apple developer site. When Xcode tools are downloaded from the OS X App store, then installation works fine. No one knows yet why there is a difference, but those who found problems resolved them by doing this (Feb, 2012).

 

ARB Main Window

10.6 - SNOW LEOPARD

Main points (following the installation instructions posted on the ARB discussion list by Matt Cottrell, in 2009):

  1. Update your OS X to 10.6, then do a disk repair (or repair permissions) using disk utility (Applications > Utilities > Disk Utility)
  2. Make sure you install the developer tools (=Xcode) and the X-windows application X11. These are on the installation disk but are not installed by default. If they are not installed then you need to do a custom install. Use the installation disc (now a dual layer DVD), begin an installation but choose to do a custom install and select only these two items (developer tools, X11).
  3. Go to the MacPorts website and read about the port system (only needs a glance)
  4. Follow their instructions to install MacPorts (downloads as a normal .dmg).
  5. After setting up macports (creates a new directory /opt), you install ARB with the following terminal command:
  6. sudo port install arb

    This will install 32-bit ARB on computers running Leopard (10.5) and 64-bit ARB on computers running Snow Leopard (10.6). I have only used it under 10.6, and it compiles easily. You can watch the files being downloaded and then compiled - it takes a little while. You get a very recent, stable, and well-tested version of ARB that can handle large datasets! It also has a few improvements while working on Macs, such as copy/paste, tabbing between windows, using the help button, displaying 3D structure models of RNA, etc.

  7. Once ARB is installed, the ARBHOME environment variable needs to be added to your PATH. The correct ARBHOME path is /opt/local/share/arb. To help you do this, the following notes are displayed on the screen after installation. If this looks like a foreign language, then ask a unix geek to help you with setting PATHs.

    **************************************************************************
    bash-users add the following lines to your ~/.profile or to your ~/.bashrc
    **************************************************************************
    ARBHOME=/opt/local/share/arb;export ARBHOME
    PATH=/opt/local/share/arb/bin:$PATH
    export PATH

    enter or copy/paste the following command (yes, the first dot is there, followed by a space):
    . ~/.profile
    2)
    **************************************************
    tcsh users add the following lines to your ~/.cshrc
    **************************************************
    setenv ARBHOME /opt/local/share/arb
    setenv PATH /opt/local/share/arb:$PATH

    enter the following command:
    source ~/.cshrc
    3)
    *********************
    enter the command arb (and return) to start ARB
    *********************

  8. In my particular case, I kept my old FINK installation of ARB on 10.5, and then installed the macports version, so I have two versions of ARB installed on the one machine. My default path is to the FINK version, and at present, when I want to start the new version I first issue the following twoTerminal command to set the path, then the arb command to start ARB:

    ARBHOME=/opt/local/share/arb;export ARBHOME;PATH=/opt/local/share/arb/bin:$PATH;export PATH

    arb

  9. Assuming everthing is installed OK, the arb command starts up the X11 shell, and then the first ARB window appears which asks you to select your ARB database. The installation comes with a small, demonstration ARB database for you to play with, found at /opt/local/share/arb.demo.arb (you have to find it in this location to open it!). So when the first ARB screen comes up, you can work through the directory lists to find and open this file to see a tree and some sequences. Then you go to the main NT window. Use the help button, find ARB tutorials, or find someone who uses ARB to learn more about what it can do for you.
  10. For serious work, you need to get sequence data files to use in the first place. I use the aligned rRNA sequence files from the SILVA web site, and/or the GreenGenes website (which is a fantastic resource!). Note that you would need a massively powerful computer to handle the entire SILVA collection of sequences, so it is better to limit yourself to the sequences you really need (ie. select those you need and download as an .arb file).

Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371

TROUBLESHOOTING (nothing ever goes right the first time, perhaps not the second...)

Am I running 32-bit or 64-bit ARB? (info from Matt Cottrell)
The 32-bit version of ARB is installed If you are using OS X 10.5.8. You need to update your OS to 10.6 in order to run the 64-bit version of ARB. You can determine if your ARB is 32- or 64-bit by doing this in terminal:

file /opt/local/bin/arb_ntree

If the 64-bit version of ARB is installed it will return the following output:

/opt/local/bin/arb_ntree: Mach-O 64-bit executable x86_64

**As to whether you are actually running in 64-bit mode, well that is currently a hot issue, as although many recent machines could do this, the apple firmware is often set to block them running 64-bit applications.

arb_tcp.dat error
By default the arb_tcp.dat is read only. So when you go to update it via Probes -> PT Server Admin -> Create Template it won’t let you edit it. This is a permissions issue, you need to change the permissions on this file so you can write to it.
To fix this, issue the following commands
cd /sw/share/arb/lib
sudo chmod g+w arb_tcp.dat

Xfig Helpfiles
XFig tries to open up its html help files in Netscape. To modify this behaviour you need to
change the settings in the Fig file which can be found at /sw/etc/app-defaults/
sudo pico -w Fig
Initial Settings:
Fig.browser: netscape –remote ‘openFile(%f)’ || netscape %f
Change to (noting the path to Safari on your computer):
Fig.browser: /Applications/safari.app/Contents/MacOS/Safari %f

You can also set the pdf reader to Preview.app using the same method.
Fig.pdfviewer: /Applications/Preview.app/Contents/MacOS/Preview %f

Searching the World Wide Web
In arb there is an option to search the world wide web. You can find it under Properties ->
Search World Wide Web (WWW). This link still refers to Netscape. Currently working on
replacing this with mozilla. (any suggestions out there??)

Extra programs to install
Install ghostview
Install this pdf/postscript viewer application to add extra functionality to arb.
fink install gv

PT-SERVER ISSUES : I'll assume you have been able to open up your database, and can see your tree. Next, to configure ARB so that it can digest this sequence database and be able to find probes or sequencing primers it needs to access the PT-server.

The PT-server is a kind of scratch file that ARB uses to store information about sequences and to greatly speed up searches for probe sequences. It also seems to cause many people grief, and there are a lot of useful posts about it on the ARB discussion list. Typically, you find that when you try to check or update your PT server you get errors that you don't have permission to write to it, or you cannot connect to the socket for that server. The first problem is sorted out quickly by finding if you have read and write permission ('ls -la'). The second issue may be because the sockets are being used by another program (I have not had this issue in Leopard). After you have successfully 'updated' your PT server, it should contain files with suffixes .ARM and .ARF.

Part of the PT-server setup is specifying a port/socket for each PT-server you want to use. For this you have to edit the file arb_tcp.dat, hidden at /sw/share/arb/lib, so the full path is: /sw/share/arb/lib/arb_tcp.dat

Open this with the sudo pico command, ie. sudo pico /sw/share/arb/lib/arb_tcp.dat

and edit the names to something more descriptive than 'usr1.arb', ie. the end of the lines

ARB_PT_SERVER0 localhost:3030 arb_pt_server -D$(ARBHOME)/lib/pts/probe_server.arb RESERVED
ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/LSU_rRNA.arb
ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/SSU-rRNA.arb

PT server error 1.
ARB Error: When saving /sw/share/arb/lib/pts/user1.arb~: Permission denied.
To fix this, check permissions on /sw/share/arb/lib/pts.
drwxr-xr-x root admin pts
Change to
drwxrwxr-x root admin pts
With the following commands
cd /sw/share/arb/lib
sudo chmod g+w pts

PT Server error 2
If you go Probes -> PT server Admin ->Check server you may get:
Trying ::1
connect to address ::1 refused
Trying 127.0.0.1
connect to address 127.0.0.1 refused
....repeated several times...
Even with this error the PT Server may still work - and complete its calculations.


Other errors? Check out the ARB discussion list archives for postings on your issue. If nothing relevant is found, ask.


After lots of work setting up ARB on pre-OS X 10.6 machines, the latest ARB is a pleasure to use, and Matt Cottrells work to get a 64-bi version packaged at macports is extremely convenient. There are many, many features in ARB. I have been using it regularly for a several years and I am constantly finding out new things it can do. Same with OSX. The combination of unix power and Apple ease of use is fascinating. Try dragging a mac file or folder into the Terminal (not X11) and see the path come up; saves a lot of hassle for copying files. Spotlight is a lot easier for me than 'grep'. You can process the trees through a powerful graphics package called XFIG (from within ARB), and you have ghostscript and ghostview to handle postscript and pdf files.

Good luck, and happy treeing! Remember, the ARB discussion list is there to help you.

Mike Dyall-Smith, Ph.D.
Max Planck Inst of Biochemistry, Martinsried Germany, 2009