Question

I’m using perlbrew and I would like to install the latest bioperl version. Should I use cpanm or git?

If git – do I just install as usual (AKA git clone ... then make and build), or should I do anything special?

UPDATE

Specifically, I’m not sure I understand the following expert from BioPerl Using Git manual:

Tell perl where to find BioPerl
(assuming you checked out the code in
$HOME/src; set this in your
.bash_profile, .profile, or .cshrc):

bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
tcsh: $ setenv PERL5LIB "$HOME/src/bioperl-live:$PERL5LIB"

Why is this necesary?

UPDATE 2

Simply exporting the bioperl cloned dir does not effect all the bp_***.pl scripts (which are usually found under /usr/bin/ after a normal Build installation).

I also tried to build from the cloned dir after switching to the correct perl version using perlbrerw, but then it runs cpan shell to install some dependencies which does not seem to work well with perlbrew (as opposed to cpanm).

So, my question remains…

Thanks!

Answer 1

The latest BioPerl is always going to be on GitHub, so git’s your answer there. Whether or not you want bleeding edge is another story, but after following the BioPerl mailing list for some time I get the feeling that the developers are more likely to say “install from GitHub” if you have any problems with BioPerl, especially since the most recent version on CPAN is from 2009. There has been a lot of development since then.

As for installing it, I don’t see why you couldn’t just go ahead and do the standard git clone ... make/build dance once you’re using your perlbrew perl, as that’s kind of the point of perlbrew. 🙂

Update for question update: The blurb about setting PERL5LIB is there because presumably BioPerl doesn’t need to be built once you’ve cloned it via git; it’s ready to use straight out of the box. Assuming you haven’t cloned it into a directory in @LIB, you need to tell Perl where to find it. You would have to do this whether or not you are using perlbrew.

Essentially the process goes like this:

1. Clone BioPerl from GitHub.
2. Make sure you’re using your perlbrew-installed Perl.
3. Set the PERL5LIB environment variable as per the BioPerl instructions.
4. Run perl -MBio::Perl -le 'print Bio::Perl->VERSION;' to make sure you’re using the BioPerl you just checked out.

Looking at the sourcecode, #4 should print out 1.006900, I think (or maybe 1.6.9, I can never keep Perl version numbers straight).