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

[Jason Stajich]

Or add a file on centos/rh to set global variables in the more modular  
way than editing /etc/profile

$ cat /etc/profile.d/perl.sh
LIBS=/usr/local/pkg/bioperl/core
if [ -z "${PERL5LIB}" ]
then
     PERL5LIB=$LIBS; export PERL5LIB
else
     PERL5LIB=$LIBS:$PERL5LIB; export PERL5LIB
fi

-jason
On Feb 3, 2010, at 11:47 AM, Mark A. Jensen wrote:

> You probably want to change the file
> /etc/profile
> (no .) --MAJ
> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 2:38 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  
> doesn't seem tochange
>
>
>> Okay,
>>> directly from the command line (don't relogin)
>>>
>>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl- 
>>> live: $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>> That gives me the correct version... For that user until I log out...
>>
>> I sudoed in to .profile and added the line directly but that  
>> doesn't  seem to have helped.
>>
>> How would I tell perl to look in the same place for Bioperl for  
>> ALL  users?
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>>
>>> Well, that's progress. It hard to debug these things remotely, but  
>>> now
>>> you can at least work around the problem by using the -I flag.  
>>> The  next
>>> weak link I would try to eliminate is the append to the .profile   
>>> file. Just
>>> do directly from the command line (don't relogin)
>>>
>>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl- 
>>> live: $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>>
>>> If this gives 1.0069, then the problem is in that append (and,  
>>> you  can also do your work!).
>>> (If you're a sudoer, I'd just edit that file directly.)
>>>
>>> cheers MAJ
>>> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca
>>> >
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, February 03, 2010 1:21 PM
>>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version   
>>> doesn't seem tochange
>>>
>>>
>>>> That gives me the 1.069 that I was wanting so the problem seems  
>>>> to  be  that perl is finding the wrong installation by default...
>>>>
>>>> Lacey
>>>>
>>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>>
>>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/ 
>>>>> bioperl-  live -le 'print Bio::Perl->VERSION;'
>>>>
>>>>
>>>
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip