[Bioperl-pipeline] biopipe files..

[Brian Osborne]

bioperl-pipeline,

I've made new versions of bioperl-pipeline-install.html, 
bioperl-pipeline-install2.html, bioperl-pipeline-run.html, and I've 
uploaded the html version of the faq. These are all on the Web site. 
It's clear that the faq is out-of-date, remember to work on faq.sgml 
and convert to faq.html using faq.pl, then rename 
bioperl-pipeline-faq.html. I'll look at this as well. Shawn and I are 
thinking about a second HOWTO mainly concerned with the XML documents 
themselves. Part 1 would concern modifying existing templates to suit 
new purposes, this is for the novice. Part 2 would discuss creating new 
xml files, de novo, this is for the more ambitious user so it will need 
to discuss the meaning of the various rules in the rules table, for 
example. Since the code is still unfrozen I think that I'll start this 
HOWTO realizing that some sections just shouldn't be written, but I'll 
try and put down an outline at least, and fill out certain parts. Any 
thoughts?

I'll also commit a text document that's just the output of mysql's 
'describe <table>' for each table in the biopipe db. No comments, but 
this could serve as a basis for a new schema description, the old one 
is missing tables. It's called database_tables.txt.

Miscellany: do the arguments to PipelineManager match up well with the 
values in PipeConf.pm? Is there a way to tell PipelineManager to use a 
local PipeConf, for example using %ENV? Guaranteed this will be a FAQ, 
"I changed my PipeConf but it stlll doesn't work!" No need to use a 
command-line argument in fact, if $ENV{PIPECONF} is defined, for 
example, then just use the value. Also, am I correct in thinking that a 
location like "~/pipe/test.fa" won't work in blast.xml?

pipeline is too cool!

Brian O.