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

[Mark A. Jensen]

I'll jump in to +1 on this; the Build will make sure you have all the necessary 
prequisites, and install those automatically (I *think* it still does this....). 
It will also do comprehensive tests. These will save MANY headaches down the 
road.

[I speak as someone who didn't build in the beginning, until one day Dave 
Messina
blithely said to me "why don't you just run ./Build test ?". Three days later, I 
was back up...]

----- Original Message ----- 
From: "Scott Cain" <scott at scottcain.net>
To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 03, 2010 2:49 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
tochange


Hi Lacey,

In order for it to be available to all users, I would suggest you go
through the "normal" installation procedure:

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

Scott


On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
<laceyanne_sanderson at shaw.ca> wrote:
> 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
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research