Bioinformatics Shared Consulting Service

Research efficiently with professional help
at affordable price

Find Out More
     

Trusted by

    

How To Install BioPerl on Mac: macOS 10.12 Sierra, OS X 10.11 El Capitan to Snow Leopard

Here is the easiest and fastest procedure to install BioPerl on Mac. 
You can't find information to install BioPerl on macOS 10.12 Sierra and OS X 10.11 El Capitan elsewhere.
If you are in a hurry, directly go to the binary package sections for your Mac. You don't need any development software such as Xcode and gcc on your Mac with this binary package.

Installation Instruction Section Menu

Binary Package Section Menu

    

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  The easiest way to install it on Mac was to use fink, because BioPerl requires many other perl modules preinstalled and fink automatically installs them.  Until Mac OS X 10.5 Leopard, fink binary package and BioPerl binary package for fink were available and it was pretty easy to install BioPerl.  However, fink binary package is not available for Mac OS X 10.6 Snow Leopard or later and it is not easy to install BioPerl on these Macs.

Building both of fink and BioPerl takes a long time.  If you do not want to spend so much time, you can use binary packages built by us. Follow the links above. 

macOS 10.12 Sierra

Even though BioPerl source package for macOS 10.12 is available in the fink database, fink package itself is not yet released for macOS 10.12.   Fortunately, our binary package for OS X 10.10 works fine on macOS 10.12.

Pre-built binary package

  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m110_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl. You need to put #!/sw/bin/perl instead of #!/usr/bin/perl in your perl script file.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.

OS X 10.11 El Capitan

Even though BioPerl source package for OS X 10.11 is available in the fink database, BioPerl could not be built due to dependencies problem.  Fortunately, binary package for OS X 10.10 works fine on OS X 10.11.

Pre-built binary package

  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m110_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl. You need to put #!/sw/bin/perl instead of #!/usr/bin/perl in your perl script file.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.

OS X 10.10 Yosemite

Preparation

Install fink

Install BioPerl

  • sudo apt-get  install bioperl-pm5162  
    This will install binary BioPerl and required perl modules. This BioPerl is for perl 5.16.2.  Yosemite has 5.16.3 and 5.18.2 perls and BioPerl won't work.

Pre-built binary package

  • It takes around 2, 3 hours to install BioPerl. If you are not familiar with command line operation or do not want to spend so much time to install BioPerl, you can use pre-built binary package.
    Just download package, extract it, and you are ready to go.
  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m110_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.

OS X 10.9 Mavericks

Preparation

  • Install Xcode 5.0.2 or later on your Mac.  Xcode is distributed in Mac App Store for free.  After installing Xcode, open Xcode and go to Xcode > Preferences > Downloads, select the Components tab, and click the button next to Command Line Tools to install necessary tools.
    Even though Command Line Tools can be installed by itself, Xcode is needed to build BioPerl.
  • Install Xquartz. Download dmg file from http://xquartz.macosforge.org/landing/ , open dmg file and install it.

Install fink

  • Download fink-0.36.1.tar.gz from http://www.finkproject.org/download/srcdist.php
  • Open Applications/Utilities/Terminal and enter commands below.
  • tar xfz fink-0.36.1.tar.gz
  • cd fink-0.36.1         
  • ./bootstrap
    Install java runtime, if asked.
    It will ask many questions.  Accept default values.
  • /sw/bin/pathsetup.sh
    It will setup environment for fink.
  • fink selfupdate-rsync
  • fink index -f

Install BioPerl

  • fink configure
    Accept default values.
  • fink selfupdate
    Accept default values.
  • fink selfupdate-rsync
  • fink index -f
  • fink scanpackages
  • fink list
    Find Package Name.  The most recent one for Mavericks is bioperl-pm5162
  • fink install bioperl-pm5162 
    Accept default values.  This will install BioPerl and required perl modules from source codes.

Pre-built binary package

  • It takes around 2, 3 hours to install BioPerl. If you are not familiar with command line operation or do not want to spend so much time to install BioPerl, you can use pre-built binary package.
    Just download package, extract it, and you are ready to go.
  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m109_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.

OS X 10.8 Mountain Lion

BioPerl source package for OS X 10.8 is not available in the fink database.  We modified binary package for Mac OS X 10.7 for OS X 10.8.  If you need BioPerl on OS X 10.8, you can use it.

Pre-built binary package

OS X 10.7 Lion

Preparation

  • Install Xcode 4.5 or later on your Mac.  Xcode is distributed in Mac App Store for free.  After installing Xcode, open Xcode and go to Xcode > Preferences > Downloads, select the Components tab, and click the button next to Command Line Tools to install necessary tools.

Install fink

  • Download fink-0.34.4.tar.gz from http://www.finkproject.org/download/srcdist.php
  • Open Applications/Utilities/Terminal and enter commands below.
  • tar xfz fink-0.34.4.tar.gz
  • cd fink-0.34.4  
  • ./bootstrap
    Install java runtime, if asked.
    It will ask many questions.  Accept default values.
  • /sw/bin/pathsetup.sh
    It will setup environment for fink.
  • fink selfupdate-rsync
  • fink index -f

Install BioPerl

  • fink configure
    Accept default values.
  • fink selfupdate
    Accept default values.
  • fink selfupdate-rsync
  • fink index -f
  • fink scanpackages
  • fink list
    Find Package Name.  The most recent one for Lion is bioperl-pm5123
  • fink install bioperl-pm51623
    Accept default values.  This will install BioPerl and required perl modules from source codes.

Pre-built binary package

  • It takes around 2, 3 hours to install BioPerl. If you are not familiar with command line operation or do not want to spend so much time to install BioPerl, you can use pre-built binary package.
    Just download package, extract it, and you are ready to go.
  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m107_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.

OS X 10.6 Snow Leopard

Preparation

Install fink

  • Download fink-0.34.4.tar.gz from http://www.finkproject.org/download/srcdist.php
  • Open Applications/Utilities/Terminal and enter commands below.
  • tar xfz fink-0.34.4.tar.gz
  • cd fink-0.34.4  
  • ./bootstrap
    Install java runtime, if asked.
    It will ask many questions.  Accept default values.
  • /sw/bin/pathsetup.sh
    It will setup environment for fink.
  • fink selfupdate-rsync
  • fink index -f

Install BioPerl

  • fink configure
    Accept default values.
  • fink selfupdate
    Accept default values.
  • fink selfupdate-rsync
  • fink index -f
  • fink scanpackages
  • fink list
    Find Package Name.  The most recent one for Lion is bioperl-pm5100
  • fink install bioperl-pm5100
    Accept default values.  This will install BioPerl and required perl modules from source codes.

Pre-built binary package

  • It takes around 2, 3 hours to install BioPerl. If you are not familiar with command line operation or do not want to spend so much time to install BioPerl, you can use pre-built binary package.
    Just download package, extract it, and you are ready to go.
  • Click here to activate your membership and download binary package. From US$29.99 only.
  • Download binary package to the Desktop.
  • Open Applications/Utilities/Terminal and enter commands below.
  • cd /; sudo tar xfz ~/Desktop/sw_m106_bp169.tgz
  • . /sw/bin/init.sh
  • Now you can use BioPerl.
  • Once you make ~/.profile and put test -r /sw/bin/init.sh && . /sw/bin/init.sh in it, you don't have to do . /sw/bin/init.sh again.