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

[Jason Stajich]

On Fri, 25 May 2001, Saurabh D. Patel wrote:

> 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.  
> 
see Bio::DB::GenBank, Bio::DB::EMBL.


> 
> 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.  
> 

I'll check but I believe they were not generated when we did the pod2html
for the website.  Will be on the todo list for the 0.7.1 release.

> 
> 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 The README file appears to be a bit out-of-date anyway.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.
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/