How-to install BioPerl on Mac OS X 10.7 “Lion”

Apple, FLOSS, Software

As my Twitter‘s followers have read in the last two weeks I had the chance to play with an early 2008′s MacPro lend to me by a friend/colleague to play with.

Since Lion has escaped ;-) nearly at the same time we took the occasion to fresh install it and reconfigure everything again for its usual bioinformatics usage.

Bio-Perl was one of the first request I had and since it was not so trivial gathering infos here’s coming this post. Official website’s project says:

Welcome to BioPerl, a community effort to produce Perl code which is useful in biology.

The official, ‘suggested’, way to install this set of tools on the OS X platform is to use the tools provided by Fink.

The Fink project wants to bring the full world of Unix Open Source software to Darwin and Mac OS X. We modify Unix software so that it compiles and runs on Mac OS X (“port” it) and make it available for download as a coherent distribution. Fink uses Debian tools like dpkg and apt-get to provide powerful binary package management. You can choose whether you want to download precompiled binary packages or build everything from source.

Unfortunately in recent years the Fink project seems to have lost some of it’s vitalità and, while the project’s still alive and working hard for 64bit’s Lion compatibility, many contributors are abbandoning the platform for various reasons. Obviously the one maintaining BioPerl is one of those.

An interesting (and appealing, at least for me) way would have been trying the use of an Homebrew‘s formula. Homebrew is a project in many ways and goals similar to Fink,but more agile and really on the growing phase. But, given the strong and extended interaction between BioPerl's packages and Perl system's importance I preferred not to mix things up and chose a 3rd way.

Sources, command-line and Perl compiler, along with CPAN were my allies.

Since the BioPerl packagas will have to be available to any user of that machine I did a global installation using administrative's privileges on the following command in Terminal.app:

perl -MCPAN -e shell

This took me to:


cpan shell -- CPAN exploration and modules installation (v1.9456)
Enter 'h' for help.
cpan[1]> d /bioperl/
Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution CJFIELDS/BioPerl-1.6.1.tar.gz
Distribution CJFIELDS/BioPerl-1.6.901.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.006900.tar.gz
Distribution CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
5 items found

and then I choose ...

cpan[2]> install C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz 

From this moment on all I had to do was to follow the suggested default's choices (and obvious customizations like the geographically based ones) and all went for the better!
:-)

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7 thoughts on “How-to install BioPerl on Mac OS X 10.7 “Lion”

  1. I do exactly this after reinstalling xcode tools and keep getting a build fail.

    Test Summary Report
    ——————-
    t/Assembly/ContigSpectrum.t (Wstat: 65280 Tests: 47 Failed: 0)
    Non-zero exit status: 255
    Parse errors: Bad plan. You planned 236 tests but ran 47.
    t/RemoteDB/SeqVersion.t (Wstat: 65280 Tests: 3 Failed: 0)
    Non-zero exit status: 255
    Parse errors: Bad plan. You planned 10 tests but ran 3.
    t/RemoteDB/SwissProt.t (Wstat: 768 Tests: 20 Failed: 3)
    Failed tests: 9-10, 20
    Non-zero exit status: 3
    t/Tools/Analysis/Protein/ELM.t (Wstat: 65280 Tests: 11 Failed: 0)
    Non-zero exit status: 255
    Parse errors: Bad plan. You planned 15 tests but ran 11.
    Files=349, Tests=21184, 376 wallclock secs ( 3.04 usr 0.98 sys + 92.02 cusr 8.36 csys = 104.40 CPU)
    Result: FAIL
    Failed 4/349 test programs. 3/21184 subtests failed.
    CJFIELDS/BioPerl-1.6.901.tar.gz
    ./Build test — NOT OK
    //hint// to see the cpan-testers results for installing this module, try:
    reports CJFIELDS/BioPerl-1.6.901.tar.gz
    Running Build install
    make test had returned bad status, won’t install without force
    Failed during this command:
    CJFIELDS/BioPerl-1.6.901.tar.gz : make_test NO

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