[Bioperl-pipeline] Notice on the modification on XMLImporter
Juguang XIAO
juguang at tll.org.sg
Tue May 11 00:04:12 EDT 2004
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
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