[Bioperl-l] Getting BioPerl from Github

tim timmcilveen at talktalk.net
Fri Oct 8 05:16:48 EDT 2010

I'm not an experienced Linux user but have been trying to download Bioperl via 
GitHub as I was getting lots of errors using the package installer. It was 
suggested by a list user that I use GitHub instead.

I installed Git using Yast.

I visited this page:

and used the installation instructions:
$ git clone git://github.com/bioperl/bioperl-live.git
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"

I tested the code:
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 
but the install didn't work.
Here is the ouput from my terminal.
tim at linux-oxgy:~> su
linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
Initialized empty Git repository in /home/tim/bioperl-live/.git/
remote: Counting objects: 88288, done.
remote: Compressing objects: 100% (23829/23829), done.
remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
Resolving deltas: 100% (66885/66885), done.
linux-oxgy:/home/tim # bash
linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live 
/usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1 
/usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
BEGIN failed--compilation aborted.
linux-oxgy:/home/tim # 

I assume that something has went wrong at this step:
To use this 'live' version of BioPerl, you need to install it (simply tell 
Perl where to find it). Assuming you checked out the code above into 
$HOME/src; set this in your .bash_profile, .profile, or .cshrc: 

How do I set things up so that the code is in $HOME/src? Where is it likely to 
be if I carried out the installation as root?

Any help would be appreciated.


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