This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
Last release: 0.7 (2005)
Argos, a.k.a. Flybase-NG, a.k.a. biodb, is designed to provide automatic replication, installation and updates of genome and organism databases and information servers, including FlyBase and euGenes. It should be not too difficult to add other organism/genome services to this replication structure.
Its main value is a collection of pre-tested and implemented common database/information service tools needed for organism database systems, which can be automatically distributed and updated to any computer.
The replication includes scripts, configurations, data, and Unix binaries for all needed programs except Perl, Java and rsync. Rsync is used as the primary distribution program.
This is server distribution system is still in development. It will be possible to use this for automated updates of mirrored servers. Uses of an automated server distribution system include local use for load distribution (apache backhand module is included for this), world-wide mirror sites for rapid local access, institution/company mirror servers for local projects and data mining. An automatable mirroring system differs from the method of providing software and data downloads by FTP in that packages of data and software in this system are kept up-to-date without human intervention. Similar package management systems such as RPM, pacman and others are well developed tools but don't quite meet the needs of this bio-database distribution.
The basic system structure is:
common/ java/ ; perl/ -- language packages servers/ -- major programs (blast, dbms, internet servers) systems/ -- operating system binaries of programs, packages docs/ -- general documents logs/ -- server logs template/ -- template information system structure flybase/ -- implemented genome information system structures eugenes/ daphnia/
This design allows segregation common infrastructure from project-specific parts. Projects may contain any needed software along with data, web docs, database files, etc. A common symbolic link folder in each project is used to access the common software structure.
Per-package installations and updates are available, to allow customer choices of packages. This includes logic to update infrastructure software from different source sites, and focuses on using rsync as primary distribution/update tool (ftp, http, others are possible; rsync has needed file-system aware updating methods).
Evaluation of RPM, pacman, cluster-backup/mirror tools, grid packaging tools found none were quite right, so a 'quick hack' perl installation program has been built.
Contents in SourceForge for this project are installation and configuration files. Subversion is not designed for storage and distribution of bulk data, program binaries, and the many package installations included in Argos repositories.
For this, argos/install/packages.conf configurations point to source servers for fetching ready-to-use packages, similar to the distribution system used by Globus.org for grid computing packages that are distributed to multiple grid node computers.
Also it is presumed that each implemented service will maintain software and documents separately from Argos, as the open-source software collected into the Argos commons are separately maintained, but installed for use with Argos.
GMOD developers can add new package sets to the argos/install/packages.conf which point to rsync servers for the packages.
Demo & Screenshots
A slide set outlines Argos/FlyBase-NG: flybase-ng-may03.pdf
These are overviews of FlyBase's server system structures.
-- flybase last-generation file system structure (1996-2002) -- all runs via Apache web server (no separate standalone servers beyond FTP) -- plus nightly cron job to FTP mirror data and software from main server -- installs and runs in any Unix path
cgi-bin/ -- web CGI programs
bin-local -> sun-sparc-solaris-bin/ -- OS specific programs
data -> ~ftp/flybase/data -- primary public data files
indices/ -- data search index files
logs/ -- web logs
mirror/ -- FTP mirroring software
server/ -- public web pages and other accessory data .etc/ -- accessory data, miscellany .srs/ -- search engine aberrations/ -- subject class folders seen in public interface anatomy/ genes/ others...
source/ -- program source code
sun-sparc-solaris-bin/ -- OS specific binaries dec-alpha-osf4-bin/ sgi-irix-bin/ linux-i86-elf-bin/
-- installation documents Install* Readme
-- 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
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:
java: axis: lsid: lucene: ogsa: xindice:
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
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:
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:
A current Unix computer, with several free Gigabytes of disk space, depending on which system packages are to be installed. The following software needs to be pre-installed on the system. Argos includes all other packages needed for its operation, drawn from common open-source software tools and packages used for bioinformatics databases and information systems.
These packages need to be and commonly are preinstalled
- Perl v5.6 or later - http://www.perl.com/
- Java v1.3 or later - http://java.sun.com/
- rsync v2.5 or later - http://rsync.samba.org/
The Argos system will replicate updates to compiled programs for these operating systems, obviating need for any human-attended compiling and installation. Unix systems that have binary package support are:
- Apple MacOSX (v10.2 build)
- Intel Linux (kernel 2.4 build)
- Sun Solaris (v8 build)
In this alpha 0.3 (june 2003) release, installation of common Argos packages uses ~ 200 MB of disk. Installation of a full FlyBase service uses ~ 2.5 GB of disk. Installation of a full euGenes service uses ~ 4 GB of disk.
See the Argos README for installation instructions.
Summary of steps to installation of an Argos server system
- Fetch the install script from a command line with
rsync rsync://flybase.net/biodb/install/installng.pl .(or use web link on this page)
perl installng.plfor summary help.
perl installng.pl -root=/usr/local/biodb -installto create root folder and fetch the installation package (location for -root= is your choice; change below steps to match)
/usr/local/biodb/install/install.conf.localto set configuration. Change package set, paths and ports as desired in this install.conf.
/usr/local/biodb/install/installng.pl -installto add the full set of packages. Packages selected from packages.conf will by copied from servers.
/usr/local/biodb/install/run-apacheto start servers
/usr/local/biodb/install/installng.pl -updateto update server periodically.