ARGOS server installation notes alpha 5 release; october 2003, d.gilbert This ARGOS system is designed for automatic installation and updates of FlyBase and other genome information servers. This 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. Server packages are (mostly) at rsync://flybase.net/argos Web notes are at http://eugenes.org/argos/ or http://flybase.net/ng/ Installation of a full FlyBase or other server will require several gigabytes of disk space. Some of these hosts have this server running http://cricket.bio.indiana.edu:8081/ -- solaris http://flybase.bio.indiana.edu:8081/ -- solaris http://chervil.bio.indiana.edu:8081/ -- linux http://marmot.bio.indiana.edu:8081/ -- macosx REQUIREMENTS ------------ Unix systems supported for binary packages: Sun Solaris v8 & v9 Intel Linux (redhat v8,9 tested) Apple MacOSX v10.2 These packages need to be and commonly are preinstalled except for Solaris v8 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/ INSTALL (with install.cgi web form) ------------------------------ This is in development; may not be fully ready yet. Use http://flybase.net/argos/install/install.cgi It is designed to handle STEP 2 below (Edit install.conf.local) INSTALL (with installargos.pl script) ------------------------------ This Perl script will handle installation installargos.pl [ options ] -info|install|list|update|reconfigure Summary of steps 0. Fetch the install script from command line with http://flybase.net/argos/install/installargos.pl OR rsync rsync://flybase.net/argos/install/installargos.pl . 1. Run installargos.pl -root=/YOUR/PATH/argos -install -v to create root folder and fetch the installation package (location for -root= is your choice; change below to match) 2. Edit /YOUR/PATH/argos/install/install.conf.local to set configuration. Change package set, paths and ports as desired in this install.conf. OR use http://flybase.net/argos/install/install.cgi 3. Run /YOUR/PATH/argos/install/installargos.pl -update to add the full set of packages. Packages selected from packages.conf will by copied from servers. 4. Run /YOUR/PATH/argos/install/run-apache to start servers The -info and -list commands make no changes to disk. All commands are benign if used with -n[orun] option. Some other installargos options: installargos.pl -info == show packages information installargos.pl -list -pack flybase == list all files in package, and required packages, from distribution servers. installargos.pl -update == update installed packages on frequent basis installargos.pl -no -install == view steps without doing them installargos.pl -root=/usr/local/argos == use new root path -------------------------------------------------- HISTORY march 2003 : changed preliminary biodb to flybase-ng may 2003 : renamed from flybaseng to argos summer 2003: added genome services: euGenes.org, daphnia-wFleaBase, centaurbase (test) fall 2003 : updates for FlyBase public server including slave servers for BLAST load balancing service; GBrowse (fb) and others -------------------------------------------------- WORKED EXAMPLE -------------- Installing all of flybase-ng may be time consuming - it still needs an easier installation script. Don't install as root -- but as a regular user, such as yourself. The basic step is to copy the installargos.pl perl script to a local folder and run are below in my test. # --------- # STEP 1 -- DOWNLOAD # http://flybase.net/flybase-ng/install/ installargos.pl # to a local folder where you want to install. # --------- dghome2% perl installargos.pl Usage: installargos.pl [ options ] -info|install|list|update|reconfigure ** 1. Run installargos.pl -install [-root=/bio/argos] == bootstrap install ** 2. Edit /bio/argos/install/install.conf.local to set configuration. 3. Run /bio/argos/install/install -install == copy server packages Packages selected from packages.conf will by copied from servers. Start web servers with /bio/argos/install/run-apache Web notes are at http://flybase.net/flybase-ng/ -- details omitted -- configuration= PACKAGES=argos-install, ROOT=/bio/argos packages= argos-install # --------- # STEP 2 -- run with parameters # IF YOU WANT TO USE default path /bio/biodb, skip the -root=... option # USE THE '-n' option to see what it will do without doing it. # --------- dghome2% perl installargos.pl -root=/Users/gilbertd/temp/argos -install -v config file missing: ./packages.conf config file missing: ./install.conf config file missing: ./install.conf.local config file missing: ./reconfigure.conf # INSTALL server directories mkdir -p /Users/gilbertd/temp/argos/install # OS=apple-powerpc-darwin # INSTALL package=argos-install # INSTALL rsync://flybase.net/argos/install/ rsync -a --exclude-from=/Users/gilbertd/temp/argos/install/rsync.exclude.local rsync://flybase.net/argos/install/ /Users/gilbertd/temp/argos/install/ cp -p /Users/gilbertd/temp/argos/install/install.conf /Users/gilbertd/temp/argos/install/install.conf.local perl -pi -e s,^ROOT=\S+,ROOT=/Users/gilbertd/temp/argos,; /Users/gilbertd/temp/argos/install/install.conf.local mkdir -p /Users/gilbertd/temp/argos/common/ ln -s ./systems/apple-powerpc-darwin /Users/gilbertd/temp/argos/common/system-local # RECONFIGURE packages dghome2% ls common/ install/ installargos.pl* # --------- # STEP 3 # EDIT BY HAND install/install.conf.local # OR see for web form configuring (in progress) # http://flybase.net/flybase-ng/install/ install.cgi # --------- # CHANGE: # path to installation ROOT=/bio/biodb # packages to install PACKAGES="biodb-root flybase" FLYBASE_CONF=#FLYBASE_CONF # TO THESE (or other desired): # path to installation ROOT=/Users/gilbertd/argos1 # packages to install PACKAGES="biodb-root flybase" FLYBASE_CONF= # --------- # STEP 4 -- run after bootstrap as install/install # -- check configuration values match above # --------- dghome2% install/install Usage: install/installargos.pl [ options ] -info|install|list|update|reconfigure 1. Run install/installargos.pl -install == bootstrap install 2. Edit /bio/biodb/install/install.conf.local to set configuration. 3. Run /bio/biodb/install/install -install == copy server packages ... configuration= APACHE_PORT=8081, DAPHNIA_CONF=#DAPHNIA_CONF, EUGENES_CONF=#EUGENES_CONF, EUGENES_PORT=7072, FLYBASE_CONF=, FLYBASE_PORT=7082, GMODWEB_CONF=#GMODWEB_CONF, PACKAGES=biodb-root flybase, PGPORT=7302, ROOT=/Users/gilbertd/argos1, TOMCAT_FLYBASE=7882, TOMCAT_PORT=7880 --------- # ACTUALLY DO THE installation for flybase... dghome2% install/install -install -v # if you want list of all files copied, use -rsopt=-v # SINCE it takes a while, dghome2% install/install -install -v >& log.install & # --------- # STEP 5 -- check installation, run web server: # --------- install/run-apache install/run-apache start # check result in logs/ folder ---------