-- flybase+ next-generation information system structure 
  -- 2003- in progress

/bio/biodb/
  common/
    java/ ; perl/ -- language packages
    servers/ -- major programs (blast, dbms, internet servers)
    systems/ -- operating system binaries of programs, packages
    
  docs/
  logs/
  
  myorg/     -- template information system structure

  flybase/   -- implemented information system structures
  eugenes/
  daphnia/
  
  
-- segregate common infrastructure from project-specific parts

-- want per-package installations and updates 
   -- allow customer choices of packages
   -- need to find/make package distribution management utility
      -- should include logic to update infrastructure software from source sites
   -- focus on 'rsync' now as main distribution tool
   -- evaluting of RPM, pacman, cluster-backup/mirror tools, 
      grid packaging tools - none quite right
   -- want CVS management of biodb structure, package info, configs 
      but not main programs, data, binaries

-- per-project packages should be fairly flexible in structure, content
   -- need to specify necessary infrastructure packages
   -- need to include security/authentication options (private and 
   public sections and methods)
   
-- retain daily mirror-ability of current server, 
   for distribution & updating of active servers to others
   and for local clusters to manage high-volume traffic
    -- more issues now with rdbms and other stand-alone server updates
    -- fixed unix path currently is used to solve configuration needs 
    -- need install/update script to allow path choices, auto-restart servers

  
-- current structure details  
/bio/biodb:

	common:
	
		java:
			axis:
			lsid:
			lucene:
			ogsa:
			xindice:
			
		perl:
			lsid:
			
		servers:
		  -- hope to use 'plain vanilla' copies of these tools so updates are easy
		     and customers can replace with own versions
		  -- customize per project and via configurations 
			apache:
			berkeleydb:
			blast:
			ldap:
			mirror:
			mysql:
			postgresql:
			rsync:
			srs:
			tomcat:
			wuftpd:
			
		source:
			apache:
				fbapache_1.3.26.tar.gz
				mod_backhand-1.2.2.tar.gz
				mod_layout-3.2.tar.gz
				mod_throttle312.tgz
			postgresql-7.3.2.tar.gz
			berkeleydb, mysql, rsync, blast, ...
			
		system-local
    -- symlink to active systems binaries for common symlinks
    		
		systems:
		-- compiled binaries for common servers
			apple-powerpc-darwin:
			intel-linux:
			sgi-irix:
			sun-sparc-solaris:
			rsync.exclude.local

	docs:

	logs:
	
	rsync.exclude
	
	
	myorg:
  -- template folder
		cgi-bin:
		common
		conf:
			apache.conf
			apache.conf.in
		data:
		etc:
		indices:
		secure:
		tmp:
		web:
		webapps:
		rsync.exclude.local
		
		
	daphnia:
  -- another genome organism

	eugenes:
  -- multi organism system

	flybase:
		cgi-bin:
		-- standard web CGI programs
		  
		common
		-- symlink to common programs
		
		conf:
			apache.conf
			apache.conf.in
			apache.conf.local
			cvsweb.conf
			
		data:
		-- public data files area, symlink to anon-FTP folder
			aberrations:
			allied-data:
			docs:
			extdb:
			genes:
			images:
			maps:
			news:
			nomenclature:
			refs:
			work:

		dbs:
			blast:
			srs:

		etc:   
		-- miscellany data, others; some should be relocated
			cytodb:
			expdb:
			gmod-fb:
			gnomap:
			icons:
			insitus:
			jdata:
			jlib:
			kevin:
			other:
			people:
			perlbio:
			pix:
			plib:
			prefs:
			sean:
			stockxgene:
			templates:
			tomcat
			transmolmaps:
			transseq:

		
		indices:
		-- data search/database files (? add postgres/mysql data here)
			blast:
			srs:

		fbwebstart.sh
		rsync.exclude.local
		tmp:

		usenet:
			bionet:
			
		web:
		--  public web interface folders
			aberrations:
			allied-data:
			alt-views:
			anatomy:
			annotfb:
			clones:
			docs:
			fbservlet:
			gbrowse_fb
			genes:
			genome-projects:
			images:
			index.html
			maps:
			people:
			pep:
			refs:
			robots.txt
			search:
			sequences:
			stocks:
			tmp
			transposons:


		webapps:
		-- standard web Servlet programs
			cvservlet:
			fbchado: