[Bioperl-l] Getting BioPerl from Github

Scott Cain scott at scottcain.net
Fri Oct 8 09:14:24 EDT 2010


Hi Tim,

Could it just be that you misspelled "bioperl-live" (as biooperl-live)
in your export statement?

Scott


On Fri, Oct 8, 2010 at 5:16 AM, tim <timmcilveen at talktalk.net> wrote:
> Hi,
> 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:
> http://www.bioperl.org/wiki/Using_Git
>
> 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
> Password:
> 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/x86_64-linux-thread-multi
> /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.
>
> Thanks,
> Tim
>
>
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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