[Bioperl-l] Getting BioPerl from Github
tim
timmcilveen at talktalk.net
Fri Oct 8 09:16:48 UTC 2010
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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