[Bioperl-l] ->add_tag_value()

Lincoln Stein lstein at cshl.edu
Mon Aug 29 15:20:50 EDT 2005


I have an environment variable in my .cshrc as follows:

	setenv PERL5LIB $HOME/projects/bioperl-live


On Friday 26 August 2005 04:08 pm, Andrew Stewart wrote:
> Do many of you use bioperl-live as your primary (or exclusive) BioPerl
> distribution, or do you keep a stable version as well?
> I'd like to use bioperl-live for instances such as this (see message
> history), but not necessarily for when I'm developing scripts that are
> going to be used by others in my lab who do not necessarily have
> bioperl-live installed.
> What I'm thinking is that I should maybe install a copy of bioperl-live
> somewhere in my personal space, and then 'use' it in certain scripts
> when needed.  I just have a few questions (these are probably more
> 'perl' questions than 'bio-perl' questions)...
> 1. Once I obtain bioperl-live via 'cvs -d :pserver etc...', do I need to
> actually go through the install routine or can I just access the modules
> from where they are downloaded?
> and
> 2. Would I then place code at the header of my script such as...
> use lib "/path/to/bioperl-live";
> use MODULE;
> and the updated module will (temporarily) override the other bioperl
> modules in my @INC?
> I tried this, actually, without any noticable change in my previous problem
> (_print_GenBank... still prints the feature tabs as
> /tab="Bio::Annotation::SimpleValue=HASH(0x87f0914)" instead of
> /tab="value"), but I don't know for certain if perl was using the
> modules from my bioperl-live installation or the older ones.
> -Andrew Stewart
> Hilmar Lapp wrote:
> >> On Aug 26, 2005, at 11:37 AM, Andrew Stewart wrote:
> >>> Would it be possible to simply update the module which contains the
> >>> error (or are there multiple files?) rather than downgrade to 1.4 or
> >>> upgrade to the HEAD branch?
> >>> -Andrew
> >
> > You could, e.g. using Jason's suggestion, but I don't know why you
> > wouldn't just want to upgrade to the main trunk. Currently, this is as
> > close as you can get to upgrading to 1.5.1., which is what you will
> > want to do anyway immediately once it's out.
> >
> >     -hilmar
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
SANDRA MICHELSEN, AT michelse at cshl.edu

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