[Bioperl-l] After Checkout of Bioperl-live version doesn't seem to change

Scott Cain scott at scottcain.net
Wed Feb 3 12:08:26 EST 2010

Hi Lacey,

Did it return "1.006" or 1.0069 exactly, which is what it should
return if you are using bioperl-live?  As for older versions of
BioPerl, if you go down the install route (which is what I generally
do), you can do the standard build procedure:

perl Build.PL
./Build test
sudo ./Build install --uninst 1

and that last part (--uninst 1) will remove older versions of the
modules installed elsewhere.  If you want to hunt down where GBrowse
installed bioperl, first you could look in the typical linuxy places,
like /usr/share/perl or /usr/lib/perl for the Bio directory, but
deleting that directory will also delete Bio::Graphics, which isn't
part of bioperl anymore.

Using PERL5LIB will put your specified bioperl at the front of the
list for when things get used, so even if you have bioperl installed
elsewhere, that one should get used.


On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
<laceyanne_sanderson at shaw.ca> wrote:
> Hi,
> I just checked out bioperl-live from svn as follows
> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
> bioperl-live
> $ echo 'export
> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
>  #adds path of bioperl-live to PERL5LIB' >> ~/.profile
> I then restarted by shell and checked the version using
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> Which returned 1.006... I am sure this is the version of bioperl I had
> previously installed and not the new one I just checked out. Is there
> something else I need to do to tell my system to disregard the old bioperl
> and instead use bioperl-live?
> I had installed BioPerl earlier using the GMOD GBrowse netinstaller although
> I can't seem to locate where it was installed. Will this effect anything? If
> so, how would I go about uninstalling it (I'm a little new to Linux)...
> By the way I am running Ubuntu Intrepid
> Thanks!
> Lacey
> _______________________________________________
> Bioperl-l mailing list
> 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

More information about the Bioperl-l mailing list