[Bioperl-pipeline] Notice on the modification on XMLImporter

[Juguang XIAO]

Hi Shawn,

On Tuesday, May 11, 2004, at 03:33  am, Shawn Hoon wrote:

> Hi Juguang,
> 	good to see some development on biopipe.
> Sorry I haven't reply to your last mail. I will try and compose one 
> soon.
> Before, u get into the XML stuff, just note that I have committed some 
> time back a
> schema based xml validation. This didn't change biopipe xml schema too 
> much, except that
> the global definition part of the xml is no longer allowed. The schema 
> definition is called pipeline.xsd in
> the xml directory and the script used to validate the xml is in 
> scripts/validate_xml.pl.

Which example|template xml can pass the validation?

> This requires
> the module: XML::Validator::Schema;
> just wanted to made sure u are aware of this.

It is always a good idea to validate the schema, but troubling users to 
download and install the supporting modules is something otherwise. 
Let's make ease for pipeline setting up first.

I will make a bundle for biopipe, (what is the current version?) with 
all dependent modules.

There are what to be bundled in. (Indent denotes the dependancy)


XML-Validator-Schema-1.06 (used by validate_xml.pl)
	Test::More 0.47
	Tree-DAG_Node-1.04
	XML-Filter-BufferText-1.01

XML-SimpleObject-0.53
	XML-LibXML-1.58
		http://xmlsoft.org/sources/libxml2-2.6.9.tar.gz (C lib)
		XML-LibXML-Common-0.12

	XML::SAX::PurePerl

Data::ShowTable

That is all so far I found. I guess it may be a bit challenging to 
install C lib in bundle. Let me try.

Come to our existing biopipe-bundle-0.1, the biopipe.sh should be 
modified to be shell-nertral. You prefer tcsh, I like bash. ;-) This 
script should not have the extension of '.sh', since it implies sh 
shell, the previous version of bash. Other projects from bioperl, 
biosql and ensembl will stay as they were.


[juguang at dhcp-21:~/Desktop/biopipe-bundle-0.1] $ ls -l
total 16
-rw-r--r--   1 juguang  admin  3247 Apr 16  2003 README
drwxr-xr-x  15 juguang  admin   510 Apr 16  2003 bioperl-db-1-1-0
drwxr-xr-x  28 juguang  admin   952 Apr 16  2003 bioperl-live
drwxr-xr-x  18 juguang  admin   612 Apr 16  2003 bioperl-pipeline
drwxr-xr-x  12 juguang  admin   408 Apr 16  2003 bioperl-run
-rw-r--r--   1 juguang  admin   194 Apr 16  2003 biopipe.sh
drwxr-xr-x   6 juguang  admin   204 Apr 16  2003 biosql-schema
drwxr-xr-x  10 juguang  admin   340 Apr 16  2003 ensembl

Regards,
Juguang

:wq