[Bioperl-pipeline] biopipe files..
Brian Osborne
brian_osborne at cognia.com
Thu Feb 20 12:35:11 EST 2003
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It's clear that the faq is out-of-date, remember to work on faq.sgml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.
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