[Bioperl-l] Installation (was Notification: i...)

[Saurabh D. Patel]

Thanks to all who replied to my previous question.  It's just as Todd
Richmond said; I installed bioperl, saw the test fail, and didnt think
to go to the tutorial for help.  

Now that my bioperl setup is working, I have another (newbie) question:
given a genbank accession number/amino acid sequence, is there any easy
way to get corresponding dna sequence?  I can think of a kludge where I
tblastn to get it, but I was wondering if there is an easier way.  If
one is browsing the ncbi entrez site, there are links on the page of a
protein sequence that accomplish this.  


Also in an unrelated minor note, the online documents refer to
Bio::Tools::Blast::Run::LocalBlast but do not have the current docs for
::StandAloneBlast.  


Saurabh.  
patels02@doc.mssm.edu


On Tue, 15 May 2001, Todd Richmond wrote:

> On 5/15/01 2:51 PM, "Peter Schattner" <schattner@alum.mit.edu> wrote:
> 
> > For what it's worth, the bioperl tutorial (bptutorial.pl) has the following
> > installation instructions:
> > 
> 
> <snip>
> 
> > If someone suggests wording to make these instructions clearer, I will
> > gladly edit the install instructions in the tutorial.
> > 
> 
> I think the problem is that people are not going to look at the tutorial
> before they install bioperl. They'll do the install, watch the tests fail,
> and wonder why. Personally, I wouldn't/didn't think to go to the tutorial to
> figure out why the tests were failing - I went straight to the .t files, and
> then to the .pm files. Setting the directory variables should be mentioned
> in the README at the root - or maybe spit out during the 'perl Makefile.PL'
> phase.
> 
good idea, let's see if we can implement that.

> The README file appears to be a bit out-of-date anyway. Part of it says:
> 

Exactly.  All are should feel free to update it to meet what you think
is
helpful to new users.  We encourage anyone to make changes to the README
to make it easier for new people to use.  Typically it is left to the
last
minute so changes now definitely are a good idea.  I'll make sure that
re-reading the README is in the todo list for the next release in case
no
one makes the changes before then.

> ---
> BUILDING THE COMPILED EXTENSIONS
> Move to the directory Compile/SW. This is where the C code and XS
> extension for the bp_sw module is held and execute these commands:
> ---
> 
> There's no longer a Compile/SW directory is there? In fact, the compiled
> extension stuff isn't even being distributed with bioperl-0.7 is it? In any
> case, I don't think the directions for the compiles extensions in any way
> resembles the actual steps you have to take.
> 
It is in bioperl-ext.  We don't distribute it with bioperl core code,
but
offer it as an extension that people may optionally install since it
probably won't work on anything but un*x.  README should definitely be
updated to reflect this.