Contact: Steven Cannon regarding this document ( cann0010-at-umn.edu )
OR bioperl-l@bioperl.org regarding Bioperl questions.
January, 2002; updates: January 2003, January 2004, January 2005 (hmm. Seems to be a pattern...)
| Overview and Introduction | |
| Bioperl | |
| CPAN | |
| Phylip | |
| NCBI Blast | |
| Clustalw | |
| t-coffee | |
| GD.pm graphics library and related stuff | |
Installing BioPerl and dependencies on OS X 10.3 is pretty easy now, making this
page close to obsolete. That's fortunate, because in the last couple of years,
finishing up a degree and starting a postdoc, I have
been over-committed, and haven't had time (or, with Fink and CPAN generally
working well, the need) to re-test all the installation
options or to maintain this page : ( I am always happy to make
additions or corrections if I get reports, however.
Basically, all you should need for the basic installation and a few key bioinformatics apps are:
OS X 10.3 uses a different default Terminal shell than 10.2 or earlier (bash rather than tcsh). Your choice of shell will change the exact instructions -- primarily, in the "run commands" file and its contents: .bash_profile and .bashrc for the bash shell, or .cshrc for tcsh.
Below this point: instructions are unfinished. Still hoping to get to a revision...
In the Bad Old Days (ca. 1999 - 2002), it was a real pain to install all of the BioPerl dependencies (the C programs and libraries that BioPerl depends on, and the bioinformatics programs such as Blast or Clustalw that BioPerl plays with). Now it's just a minor annoyance. Most of the dependencies are taken care of by the CPAN Bundle::BioPerl. Kinks have been worked out of many OS X bioinformatics installations, and some of them are available through ports at Fink or bioteam.net/MacOSX/. Or, if you go in for masochism, you can still install each dependency manually. For the masochistic route, my old 2002 notes may be of some help, though many distributions and patches and other details have probably changed. So, if you happen to use the old instructions, please don't look to me for company for your misery. On the other hand, I would be happy to get suggestions for improving the current instructions-in-progress.
A lot of things have changed between 10.2 and 10.3. This includes the default Terminal shell, so I am still feeling my way and making a lot of adjustments. Therefore, these are very early-stage instructions. Please bear with me...
One more piece of advice before you commence installations: much of this software is under active development, and there are lots of packages, and you will be installing lots of stuff with "superuser" priveledges. You can do some serious damage to your system.
A couple of FAQs:
I type "make blablabla" and get the message "make: Command not found.".
You need to install the OS X "Xcode tools." When you get to the "Installation Type"
step, choose "Customize" and include at least the Developer Tools Software,
the Mac OS X SDK, the BSD SDK, and the X11 SDK. (If you're in 10.1 and 10.2, install
the "Developer CD").
Will BiopPerl and dependencies install under OS 10.1 or 10.2?
[I HOPE you aren't using 10.1 or 10.2...] Yes, but a few details have changed. The default user shell before
10.3 was tcsh, and is bash in 10.3. (That's not a fundamental change:
you can change your preferred shell in Terminal Preferences: have the
system execute the /bin/tcsh file, or if your account is managed centrally,
have your OS X sysadmin set the preference in Workgroup Manager.)
The GD install is different in 10.3.
The basic installation of Bioperl on OS X goes without a hitch.
Installation of the dependent packages and associated programs
sometimes takes a little thought, or a small trick -- maybe just setting an environment
variable or updating a symbol table, but enough to cause someone new to the
Unix installation process some grief.
Setting up .bash_profile
First, check whether .bash_profile exists. Start the terminal application, then
cd ls -la
If you don't see .bash_profile, create it. Here is what is currently in my file. It is rather hacky, and I have stuffed commands into .bash_profile rather than splitting them off into .bashrc, but this seems to work for now. BTW, see a lot more info on what should go into these files at
You should be able to copy this using pico:
pico .bash_profile
Then type or cut and paste the following. Note that some paths will need to be changed, and you may need to point to different applications. This file also turns on color listing in the Terminal.
# source .bashrc if it's there if [ -f ~/.bashrc ]; then . ~/.bashrc fi # turn on color file listing export CLICOLOR=1 # -l = list view # -a = all views, even hidden # -h = human-readable sizes, e.g. 900B, 15K, 1.2MB alias ll="/bin/ls -lah" # keeps pico from line wrapping alias pico="/usr/bin/pico -w" # paths to some bioinf applications PATH=$PATH:/usr/local/biotools/bin PATH=$PATH:/Applications/bioinf/phylip/exe PATH=$PATH:/Applications/bioinf/t_coffee PATH=$PATH:/usr/local/biotools/bin export PATH export BLASTDIR=/usr/local/biotools/bin export BLASTDB=/Users/YOURHOME/data/blast export MANPATH=/usr/local/biotools/man export WISECONFIGDIR=/usr/local/biotools/wisecfg/ export EMBOSS_ACDROOT=/usr/local/biotools/share/EMBOSS/acd
then exit pico and save. Now, make Darwin see your changes, either by quitting Terminal and starting it up again, or by going:
source .bash_profileReturn to top
Download and unzip a BioPerl distribution from Bioperl.org.
You can install it immediately to get some instant gratification
(many parts will work without anything else), and then do the
tedious work of installing some or all of the other programs that parts of
Bioperl use or depend on, such Blast.
The bioperl installation requires root access, which you will get using the
'sudo' command and your password. After 'make test', don't worry if a number
of the tests fail, but note which additional packages are recommended --
and why. You may not need all of the "extras".
cd bioperl-x.x more README perl Makefile.PL make make test sudo make install
As the "Bioperl external package dependencies" page explains (http://www.bioperl.org/Core/external.shtml),
"Bioperl contains wrappers, parsers and modules that can make use of several third party applications. Parts of our pre-install test suite may try to check for the presence and behaviour of these applications so you may see mention of them during the bioperl 'make test' installation step. Don't worry about them if you don't need or or use them."
Nevertheless, many of the third party applications, extensions, and modules are important, so here are some detailed OS X installation notes. These instructions follow the order in which dependencies are discussed at "Bioperl external package dependencies" page. All of the extensions and modules (but not third party applications) are conveniently available from ftp://bioperl.org/pub/external/ (though sometimes in as less-than-current versions).
Return to topInstall CPAN shell sudo perl -MCPAN -e shell; install Bundle::BioPerl
After the CPAN Bundle::Bioperl installation, read bptutorial.pl, and try running some of the sample programs:
perl bptutorial.pl perl bptutorial.pl 4 perl bptutorial.pl 0
With the last command, you will get a number of errors, unless you have installed the dependencies. That is the next step -- depending on what functionality you actually need from Bioperl.
Return to topInstall binaries from http://bioteam.net/MacOSX/ per their directions. First thing to do: sudo mkdir /usr/local/biotoolsReturn to top
PHYLIP 3.6, called 3.6a3 from
http://evolution.genetics.washington.edu/phylip/phylip36.html
Return to top
Download the software from http://www.embl.de/~chenna/clustal/darwin/ Follow instructions.Return to top
Download T-COFFEE from
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
Then place in bioinf, rename to 't_coffee', then gunzip and untar, and ...
cd t_coffee ./install
/Applications/bioinf/t_coffee/bin \Return to top
Partial notes for installing GD.pm (GD-2.11) on OS X 10.3:
See notes at: http://www.paginar.net/matias/articles/gd_x_howto.html mostly worked fine but needed to do sudo mkdir /usr/local/man/man1/ Also, I got errors related to freetype, ending with these messages: ... gdft.c:1112: error: `bm' undeclared (first use in this function) gdft.c:1112: error: parse error before "image" make[2]: *** [gdft.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 Try configuring without freetype: ./configure --without-freetype make sudo make install Libraries were installed in: /usr/local/lib cd GD-2.11/ perl Makefile.PL Build JPEG support? [y] Build FreeType support? [y] n Build XPM support? [y] ... Now, re-do the CPAN installation of Bundle::BioPerl to specify where gd lives... Where is libgd installed? [/usr/lib] /usr/local/lib Please choose the features that match how libgd was built: Build JPEG support? [y] Build FreeType support? [y] n Build XPM support? [y]Return to top