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Difference between revisions of "Argos"
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+ | ==Status== | ||
+ | |||
+ | Actively supported | ||
+ | |||
+ | Last release: 0.7 (2005) | ||
+ | |||
+ | ==Contact== | ||
+ | |||
+ | [mailto:argos@eugenes.org argos@eugenes.org] | ||
+ | |||
==Description== | ==Description== | ||
Line 31: | Line 41: | ||
==Developer notes== | ==Developer notes== | ||
− | Current developers are Don Gilbert, Nihar Sheth and Victor Strelets for FlyBase-NG and euGenes uses. We hope others will try it and join us in using and developing it. Email us at argos@eugenes.org | + | Current developers are [[User:Dongilbert|Don Gilbert]], Nihar Sheth and Victor Strelets for FlyBase-NG and euGenes uses. We hope others will try it and join us in using and developing it. Email us at [mailto:argos@eugenes.org argos@eugenes.org]. |
− | Contents in | + | Contents in {{SF_SVN|argos|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. | + | For this, <tt>argos/install/packages.conf</tt> 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. | 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. | + | GMOD developers can add new package sets to the <tt>argos/install/packages.conf</tt> which point to rsync servers for the packages. |
==Demo & Screenshots== | ==Demo & Screenshots== | ||
− | Genome information systems running in Argos are at http://flybase.net/flybase-ng/ | + | <!-- Don, this link does not work anymore: |
− | + | Genome information systems running in Argos are at http://flybase.net/flybase-ng/ | |
+ | --> | ||
A slide set outlines Argos/FlyBase-NG: [[Media:Flybase-ng-may03.pdf|flybase-ng-may03.pdf]] | A slide set outlines Argos/FlyBase-NG: [[Media:Flybase-ng-may03.pdf|flybase-ng-may03.pdf]] | ||
Line 55: | Line 66: | ||
====Last generation==== | ====Last generation==== | ||
− | -- flybase last-generation file system structure (1996-2002) | + | -- flybase last-generation file system structure (1996-2002) |
-- all runs via Apache web server (no separate standalone servers beyond FTP) | -- 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 | -- plus nightly cron job to FTP mirror data and software from main server | ||
-- installs and runs in any Unix path | -- installs and runs in any Unix path | ||
− | + | ||
− | (any)/flybase-server/ | + | (any)/flybase-server/ |
− | + | ||
cgi-bin/ -- web CGI programs | cgi-bin/ -- web CGI programs | ||
− | + | ||
bin-local -> sun-sparc-solaris-bin/ -- OS specific programs | bin-local -> sun-sparc-solaris-bin/ -- OS specific programs | ||
− | + | ||
data -> ~ftp/flybase/data -- primary public data files | data -> ~ftp/flybase/data -- primary public data files | ||
− | + | ||
indices/ -- data search index files | indices/ -- data search index files | ||
− | + | ||
logs/ -- web logs | logs/ -- web logs | ||
− | + | ||
mirror/ -- FTP mirroring software | mirror/ -- FTP mirroring software | ||
− | + | ||
server/ -- public web pages and other accessory data | server/ -- public web pages and other accessory data | ||
.etc/ -- accessory data, miscellany | .etc/ -- accessory data, miscellany | ||
.srs/ -- search engine | .srs/ -- search engine | ||
aberrations/ -- subject class folders seen in public interface | aberrations/ -- subject class folders seen in public interface | ||
− | anatomy/ | + | anatomy/ |
− | genes/ | + | genes/ |
others... | others... | ||
− | + | ||
source/ -- program source code | source/ -- program source code | ||
− | + | ||
sun-sparc-solaris-bin/ -- OS specific binaries | sun-sparc-solaris-bin/ -- OS specific binaries | ||
dec-alpha-osf4-bin/ | dec-alpha-osf4-bin/ | ||
sgi-irix-bin/ | sgi-irix-bin/ | ||
− | linux-i86-elf-bin/ | + | linux-i86-elf-bin/ |
− | + | ||
-- installation documents | -- installation documents | ||
Install* | Install* | ||
Line 96: | Line 107: | ||
− | -- flybase+ next-generation information system structure | + | -- flybase+ next-generation information system structure |
-- 2003- in progress | -- 2003- in progress | ||
− | + | ||
/bio/biodb/ | /bio/biodb/ | ||
common/ | common/ | ||
Line 104: | Line 115: | ||
servers/ -- major programs (blast, dbms, internet servers) | servers/ -- major programs (blast, dbms, internet servers) | ||
systems/ -- operating system binaries of programs, packages | systems/ -- operating system binaries of programs, packages | ||
− | + | ||
docs/ | docs/ | ||
logs/ | logs/ | ||
− | + | ||
myorg/ -- template information system structure | myorg/ -- template information system structure | ||
− | + | ||
flybase/ -- implemented information system structures | flybase/ -- implemented information system structures | ||
eugenes/ | eugenes/ | ||
daphnia/ | daphnia/ | ||
− | + | ||
− | + | ||
-- segregate common infrastructure from project-specific parts | -- segregate common infrastructure from project-specific parts | ||
− | + | ||
− | -- want per-package installations and updates | + | -- want per-package installations and updates |
-- allow customer choices of packages | -- allow customer choices of packages | ||
-- need to find/make package distribution management utility | -- need to find/make package distribution management utility | ||
-- should include logic to update infrastructure software from source sites | -- should include logic to update infrastructure software from source sites | ||
-- focus on 'rsync' now as main distribution tool | -- focus on 'rsync' now as main distribution tool | ||
− | -- evaluting of RPM, pacman, cluster-backup/mirror tools, | + | -- evaluting of RPM, pacman, cluster-backup/mirror tools, |
grid packaging tools - none quite right | grid packaging tools - none quite right | ||
− | -- want CVS management of biodb structure, package info, configs | + | -- want CVS management of biodb structure, package info, configs |
but not main programs, data, binaries | but not main programs, data, binaries | ||
− | + | ||
-- per-project packages should be fairly flexible in structure, content | -- per-project packages should be fairly flexible in structure, content | ||
-- need to specify necessary infrastructure packages | -- need to specify necessary infrastructure packages | ||
− | -- need to include security/authentication options (private and | + | -- need to include security/authentication options (private and |
public sections and methods) | public sections and methods) | ||
− | + | ||
− | -- retain daily mirror-ability of current server, | + | -- retain daily mirror-ability of current server, |
for distribution & updating of active servers to others | for distribution & updating of active servers to others | ||
and for local clusters to manage high-volume traffic | and for local clusters to manage high-volume traffic | ||
-- more issues now with rdbms and other stand-alone server updates | -- more issues now with rdbms and other stand-alone server updates | ||
− | -- fixed unix path currently is used to solve configuration needs | + | -- fixed unix path currently is used to solve configuration needs |
-- need install/update script to allow path choices, auto-restart servers | -- need install/update script to allow path choices, auto-restart servers | ||
− | + | ||
− | + | ||
− | -- current structure details | + | -- current structure details |
/bio/biodb: | /bio/biodb: | ||
− | + | ||
common: | common: | ||
− | + | ||
java: | java: | ||
axis: | axis: | ||
Line 151: | Line 162: | ||
ogsa: | ogsa: | ||
xindice: | xindice: | ||
− | + | ||
perl: | perl: | ||
lsid: | lsid: | ||
− | + | ||
servers: | servers: | ||
-- hope to use 'plain vanilla' copies of these tools so updates are easy | -- hope to use 'plain vanilla' copies of these tools so updates are easy | ||
and customers can replace with own versions | and customers can replace with own versions | ||
− | -- customize per project and via configurations | + | -- customize per project and via configurations |
apache: | apache: | ||
berkeleydb: | berkeleydb: | ||
Line 170: | Line 181: | ||
tomcat: | tomcat: | ||
wuftpd: | wuftpd: | ||
− | + | ||
source: | source: | ||
apache: | apache: | ||
Line 179: | Line 190: | ||
postgresql-7.3.2.tar.gz | postgresql-7.3.2.tar.gz | ||
berkeleydb, mysql, rsync, blast, ... | berkeleydb, mysql, rsync, blast, ... | ||
− | + | ||
system-local | system-local | ||
-- symlink to active systems binaries for common symlinks | -- symlink to active systems binaries for common symlinks | ||
− | + | ||
systems: | systems: | ||
-- compiled binaries for common servers | -- compiled binaries for common servers | ||
Line 190: | Line 201: | ||
sun-sparc-solaris: | sun-sparc-solaris: | ||
rsync.exclude.local | rsync.exclude.local | ||
− | + | ||
docs: | docs: | ||
− | + | ||
logs: | logs: | ||
− | + | ||
rsync.exclude | rsync.exclude | ||
− | + | ||
− | + | ||
myorg: | myorg: | ||
-- template folder | -- template folder | ||
Line 213: | Line 224: | ||
webapps: | webapps: | ||
rsync.exclude.local | rsync.exclude.local | ||
− | + | ||
− | + | ||
daphnia: | daphnia: | ||
-- another genome organism | -- another genome organism | ||
− | + | ||
eugenes: | eugenes: | ||
-- multi organism system | -- multi organism system | ||
− | + | ||
flybase: | flybase: | ||
cgi-bin: | cgi-bin: | ||
-- standard web CGI programs | -- standard web CGI programs | ||
− | + | ||
common | common | ||
-- symlink to common programs | -- symlink to common programs | ||
− | + | ||
conf: | conf: | ||
apache.conf | apache.conf | ||
Line 233: | Line 244: | ||
apache.conf.local | apache.conf.local | ||
cvsweb.conf | cvsweb.conf | ||
− | + | ||
data: | data: | ||
-- public data files area, symlink to anon-FTP folder | -- public data files area, symlink to anon-FTP folder | ||
Line 247: | Line 258: | ||
refs: | refs: | ||
work: | work: | ||
− | + | ||
dbs: | dbs: | ||
blast: | blast: | ||
srs: | srs: | ||
− | + | ||
− | etc: | + | etc: |
-- miscellany data, others; some should be relocated | -- miscellany data, others; some should be relocated | ||
cytodb: | cytodb: | ||
Line 275: | Line 286: | ||
transmolmaps: | transmolmaps: | ||
transseq: | transseq: | ||
− | + | ||
− | + | ||
indices: | indices: | ||
-- data search/database files (? add postgres/mysql data here) | -- data search/database files (? add postgres/mysql data here) | ||
blast: | blast: | ||
srs: | srs: | ||
− | + | ||
fbwebstart.sh | fbwebstart.sh | ||
rsync.exclude.local | rsync.exclude.local | ||
tmp: | tmp: | ||
− | + | ||
usenet: | usenet: | ||
bionet: | bionet: | ||
− | + | ||
web: | web: | ||
-- public web interface folders | -- public web interface folders | ||
Line 314: | Line 325: | ||
tmp | tmp | ||
transposons: | transposons: | ||
− | + | ||
− | + | ||
webapps: | webapps: | ||
-- standard web Servlet programs | -- standard web Servlet programs | ||
Line 341: | Line 352: | ||
==Documentation== | ==Documentation== | ||
− | '''Quick start:''' | + | '''Quick start:''' |
− | + | See the [http://gmod.svn.sourceforge.net/viewvc/gmod/argos/trunk/install/README.txt?revision=HEAD Argos README] for installation instructions. | |
− | + | ||
− | + | ||
Line 357: | Line 366: | ||
# Run <code>/usr/local/biodb/install/run-apache</code> to start servers | # Run <code>/usr/local/biodb/install/run-apache</code> to start servers | ||
# Run <code>/usr/local/biodb/install/installng.pl -update </code> to update server periodically. | # Run <code>/usr/local/biodb/install/installng.pl -update </code> to update server periodically. | ||
+ | |||
==Downloads== | ==Downloads== | ||
− | * Argos-based servers:http:// | + | * Argos-based servers: http://eugenes.org/argos/ for euGenes genome database, and other services in development. |
− | * Main package distribution: [rsync:// | + | * Main package distribution: [rsync://eugenes.org/argos] |
* With project-specific packages distributed from other servers, as specified in the [http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/argos/install/packages.conf?rev=HEAD argos/install/packages.conf] | * With project-specific packages distributed from other servers, as specified in the [http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/argos/install/packages.conf?rev=HEAD argos/install/packages.conf] | ||
− | [[GMOD Components]] | + | [[Category:Database Tools]] |
+ | [[Category:GMOD Components]] | ||
+ | [[Category:WFleaBase]] |
Latest revision as of 15:41, 16 July 2012
Contents
Status
Actively supported
Last release: 0.7 (2005)
Contact
Description
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.
Developer notes
Current developers are Don Gilbert, Nihar Sheth and Victor Strelets for FlyBase-NG and euGenes uses. We hope others will try it and join us in using and developing it. Email us at argos@eugenes.org.
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
Flybase Servers
These are overviews of FlyBase's server system structures.
Last generation
-- 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
(any)/flybase-server/
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
Next Generation
-- 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:
Requirements
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.
Documentation
Quick start:
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) - Run
perl installng.pl
for summary help. - Run
perl installng.pl -root=/usr/local/biodb -install
to create root folder and fetch the installation package (location for -root= is your choice; change below steps to match) - Edit
/usr/local/biodb/install/install.conf.local
to set configuration. Change package set, paths and ports as desired in this install.conf. - Run
/usr/local/biodb/install/installng.pl -install
to add the full set of packages. Packages selected from packages.conf will by copied from servers. - Run
/usr/local/biodb/install/run-apache
to start servers - Run
/usr/local/biodb/install/installng.pl -update
to update server periodically.
Downloads
- Argos-based servers: http://eugenes.org/argos/ for euGenes genome database, and other services in development.
- Main package distribution: [rsync://eugenes.org/argos]
- With project-specific packages distributed from other servers, as specified in the argos/install/packages.conf