BioPerl Tutorial: Install BioPerl on Windows

bioperl tutorial
In my last article I covered importance of BioPerl in Bioinformatics and why Perl is popular among Bioinformaticians. This article in BioPerl Tutorial series is dedicated on how to install BioPerl on Windows. My computer has Windows 7 so I will be teaching on how to install BioPerl on Windows 7. I though assume same steps will be applicable on other Windows version (though few might need couple of tweaks).

BioPerl Installation:

To install BioPerl, we need to have Perl on our system. Thus, we will be covering on how to install Perl on Windows and then will move to BioPerl installation.

Installing Perl

To install Perl, you should have it on your system. You can download Perl from internet but make sure you download ActivePerl 5.8.8.819 or higher version. Only this version is supported by BioPerl Team.

 Why ActivePerl 5.8.8.819 or higher only?

The main reason behind using versions equal or after of 5.8.8.819 is inclusion of Perl Package Manager 4 (abbreviated as PPM4). PPM4 is far better than its earlier versions and also has a GUI interface (which makes thing easier for windows users who don’t have knack in remembering, typing and executing commands).

One can download ActivePerl community edition from http://www.activestate.com/activeperl/downloads or from my own site (version 5.14.2 for 64 bit computers). This is the version on which I will be installing and using BioPerl further.

  •  First Step:

Once download is completed, after opening the installation package, one will see following screenshot and you need to click on next.

bioperl installation guide 1

  • Second Step:

    a)     After accepting user agreement, feature selection window will pop-up. If you don’t have much knowledge which features you need and which don’t, just click next and all features will be installed.

install bioperl 2

b)     One can give custom path to perl directory by clicking Browse button

bioperl tutorial 3

  • Third Step:

Ensure to choose all the three options in Setup options or else you might face problems later on.

bioperl modules 4

Then click on click install button and if all goes well, you will see initiation of activeperl installation on your system.

perl installation 5

After sometime (depending on your configuration), you will see following screen which informs you that installation of active Perl is complete.

activeperl installation 6

After clicking on finish, you will see release notes:

active perl installation 7

Now it’s the time to install BioPerl. We will be installing BioPerl as well as BioPerl modules through PPM.

 

 GUI Installation of BioPerl:

  •  Step 1:

To install BioPerl you need to run Perl application you have just installed. You can open it from Start Menu.

perl tutorial 8

After opening ActivePerl folder, you will see PPM icon. Double click to open it.

installing perl 9

  • Step 2:

Now PPM will open up. It will begin sync with PPM database and once it is done (it might take time depending on your internet connection), you are all set to install BioPerl.

NOTE: This step requires active internet connection.

perl package manager 1

  • Step 3:

Go to EDIT and then Preferences. Click on Repositories tab. Following window will open up.

bioperl installation screenshot 11

  • Step 4:

Add following repositories:

Name Location
BioPerl-Regular Releases http://bioperl.org/DIST
BioPerl-Release Candidates http://bioperl.org/DIST/RC
Kobes http://cpan.uwinnipeg.ca/PPMPackages/10xx/
Bribes http://www.bribes.org/perl/ppm
Trouchelle http://trouchelle.com/ppm10

 

bioperl screenshot 12

Once call repositories are added you can see those in repositories list:

bioperl tutorial 13

Now click on Ok to close repositories window.

  •  Step 5

Go to view and select all packages

install bioperl 14

  • Step 6:

In the search box, write bioperl and you will see BioPerl packages.

bioperl modules 15

  • Step 7:

Right click on version available of BioPerl and select install.
install bioperl 16

  • Step 8:

Now will see the BioPerl is marked for installation. To install BioPerl you need to click on Green Arrow.

bioperl installation tutorial 17

You will see following screen now and click on Ok.

bioperl guide 17

 

This will initiate installation of BioPerl on your system.

After few minutes (depending on your internet screen), you will see application window where it will say BioPerl is installed on ‘site’.

bioperl installation tutorial 18

 

Congrats! You have sucessfully installated BioPerl on your system.

I hope this BioPerl installation tutorial will give you better idea on how to install BioPerl on Windows using GUI interface of PPM. Next article will cover how to write BioPerl script.

 

About Brij

Bhrat Brij is a SEO expert, Internet Marketer, Affiliate Marketer and Bioinformatician. My short bio or have a look on my Google Profile

Comments

  1. pawan says:

    Dear Bhrat
    I am little bit new in bioperl. so after installation of your above steps I could not run some of my script. which inclouds Blast.pm and BeginPerlBioinfo.pm module. This .pm file is not there in this folder

    Perl64\site\lib\Bio\Tools.

    Kindly help me.

    With best regards,
    pawan.

    • Brij says:

      Hello Pawan,

      I was on holidays and could not get online.

      Can you please let me know if you still need my help?

      Thanks,
      Bhrat

Trackbacks

  1. [...] the next article on this BioPerl tutorial series, we will see how to install BioPerl in Windows as well as on Linux [...]

  2. [...] Program or BioPerl Script. If you are looking for BioPerl Introduction and Usage, click here and to install BioPerl you can see this BioPerl tutorial for windows [...]

  3. [...] Install BioPerl on Windows [...]

Speak Your Mind

*