[Bioperl-pipeline] Hi, there! Just ignore this message.

[Brian Osborne]

Sang,

You're correct, it's complex. But the good news is you don't necessarily
have to understand everything about it in order to use it. In my opinion the
single most important thing is the XML file. I've started a HOWTO document
that's supposed to talk about the XML files, and I've just put an unfinished
version of the HOWTO on the Web:

http://www.biopipe.org/docs/howto/html/biopipe_xml.html

Why don't you take a look at it, tell me what you think.

Here's how you should get started, in my opinion. First, do the installs, as
outlined in http://www.biopipe.org/bioperl-pipeline-install.html. Then try a
simple pipeline, local mode, like xml/templates/blast_file_pipeline.xml. If
you can get a simple one to run then you'll begin to see that it's not as
bad as it looks.


Brian O.


-----Original Message-----
From: bioperl-pipeline-bounces at bioperl.org
[mailto:bioperl-pipeline-bounces at bioperl.org]On Behalf Of Sang Chul Choi
Sent: Wednesday, March 12, 2003 4:03 AM
To: bioperl-pipeline at bioperl.org
Subject: [Bioperl-pipeline] Hi, there! Just ignore this message.

Dear Pipeline Developers!

When I met bioperl-pipeline, it was thought to be what I wanted for my
current project.
Pipeline almost automatically processes sequences into various other
outputs.
Pipeline, its name literally explained what it will do for me.

Great! Just great!

After a long investigation into biopipe source, I have fallen into deep
depression.
Is it difficult for me to understand biopipe? Yes, it was and is. Maybe it
will be.

Database schema, database adaptor classes, various core classes such as Job,
Input, Manager, ...

My last door to understanding of biopipe is:
"How does RunnableDB work?"
It involves RunnableI, RunnableI derived classes (DataMonger, RepeatMasker,
Blast),
again Job, Input,...

Plus, I don't know what rule of jobs mean: COPY_ID, COPY_INPUT, CREATE_INPUT
(not implemented yet),
UPDATE, WAITFORALL, WAITFORALL_AND_UPDATE.

I am very tired with these pipeline sources. I want to just give up.

But, I will NOT do that, because pipeline has wonderful functionalities.

Sincerely yours,

good night!

Sang Chul Choi

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