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

Jonathan Epstein Jonathan_Epstein at nih.gov
Wed Feb 3 13:40:56 EST 2010

Here's a low-tech answer: if I'm having a problem like this with my 
PERL5LIB environment variable [Perl is not doing what I /think/ I've 
told it to do], I try to figure out where Perl is actually looking.

So in this case I'd write a two-line BioPerl program foo.pl like:

    use Bio::Perl;
    $seq_object = get_sequence('swiss',"ROA1_HUMAN");

Start the debugger with "perl -d:ptkdb foo.pl", set a breakpoint before 
line 2, run to that breakpoint, and then step-in with the debugger and 
see in which directory the corresponding source file resides.

My guess is that there are additional subordinates paths within 
/usr/local/share/applications/Bioperl/bioperl-live which must be added 
to your path.



On 2/3/2010 12:58 PM, Chris Fields wrote:
> If I were to choose a versioning scheme I would probably go with simple bipartite ones, but (by legacy) BioPerl is based on the perl tripartite versioning scheme:
> http://www.perl.com/pub/a/2000/04/whatsnew.html#Version_Tuples
> For instance, with perl 5.10.1 the vstring v5.10.1 would be 5.010001.  BioPerl 1.6.0 is 1.006000, so you either have an older lingering CPAN installation of 1.6.0 or you are installing that one (I'm guessing the former, as the latest from CPAN is now 1.6.1, or 1.006001).  Effectively, svn trunk is v1.6.900 (roughly the 900th point release).
> The reason trunk is set at 1.6.9 is simple, it supercedes any current CPAN release version, and it's very unlikely we'll release another 898 point releases of BioPerl.  It also tags the main trunk as pre-1.7.  I can cherry-pick off trunk into the properly designated 1.6 branch (now at 1.6.1), bump the release there, and push to CPAN.  Once we actively start on 1.7 we'll probably bump trunk up to something higher.  It also enables one to distinguish between a CPAN release of BioPerl vs. the SVN version, as installing from svn has unfortunately become very common practice.  Comes in useful in cases like yours, where we're trying to distinguish what version is being called.
> chris
> On Feb 3, 2010, at 11:32 AM, Lacey Sanderson wrote:
>> 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?
>> Lacey
>> 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:$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
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
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>> Bioperl-l at lists.open-bio.org
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