[Bioperl-pipeline] getting your example to work

[Andy Nunberg]

Hi,
I have  abit of 'free' time so I thought I would get on running your
pipeline-example.
In your website you stay to execute the following within the bioperl-pipeline
directory
perl Xml2DB.pl -dbname annotate_pipeline -p
templates/genomic_sequence_annotation.xml

I am having problems with Xml2DB.pl, just running on its own does not work. I
found out I do not have XML parser and XML simple object modules.  You may want
to update your website to state you need these modules.

I downloaded both only to find out I need to download expat.  I am unable to do
an install , i get some error in XML simple object how there is some 'rule'
missing etc....

SO i decided just to put everything in one directory and update my PERLLIB
variable.

Now if i just run Xml2DB.pl I got the following
Can't locate XML/Parser/Expat.pm in @INC....
Compilation failed in require at Xml2Db.pl line 7

As it turns out Expat.pm is located in XML/Expat/Expat.pm 
at least it is in the version of XML parser i just got from CPAN 
(XML-Parser-2.31) I had to make soft link to XML so the first use statement of
Xml2SB.pl would not return
an error

You may want to check your code against a new install of XML parser etc.. to
make sure it still works.
I can start switching the use statements, but then I am afraid you may  have a
call later on that will not work...
or I can just put Expat.pm where the script thinks it ought to be.  Either way
you will need to let people know about this if they have to install the XML
modules
*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com