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

Lacey Sanderson laceyanne_sanderson at shaw.ca
Wed Feb 3 12:32:47 EST 2010

It returned "1.006"... unfortunately no 9 at the end... Any idea why  
it doesn't seem to be picking up the bioperl-live checkout?

PS. Why do the distributions have version numbers like 1.5.2 and 1.6  
and yet the bioperl-live (which I take to be the most current version  
of bioperl) returns 1.069?


On 3-Feb-10, at 11:08 AM, Scott Cain wrote:

> 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
> ./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.
> Scott
> 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: 
>>  #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

Lacey Sanderson
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.

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