| Hi All, | | I've been trying to carry out a flybase installation for Êa week or two but it | keeps failing, and I'm not sure why. I'm wondering if you could give me a coupl | eof pointers? | | First problem is related to the install.conf and the install.local.conf files | (attached). I generate the files from the install.cgi webpage, and save them | into the /bioi/argos/install directory. | | I then type Ê./install/install -install -v Ê(the installation kicks off, but it | appears that the install.conf file gets overwrttien -ie,. the gmod dissapears | from the PACKAGES line)? I've tried removing the install.conf file, but it keeps | coming back when I start the installation. > the install.conf file gets overwrttien This is correct; install.conf.local is the file with your local configurations which override install.conf. This installer is sensitive to steps outlined at http://flybase.net:8081/install/install.cgi At step (2), a very basic file set is created and a few install files fetched from flybase. This should be done in an otherwise empty directory. If you use default path, that would be /bio/argos/. The next step (3) is to create your local configuration with the web form. You need to place this file into your {argosroot}/install/ folder as "install.conf.local" This file overrides the default settings of install.conf, which is always mirrored. Any "*.local" configuration file is treated this way by the installargos.pl updater. So it is right that install/install.conf is mirrored, your settings need to be in file install/install.conf.local. The GMOD package is one that I haven't tested or updated recently -- it should contain some parts of GMOD.org software for general database uses, but it isn't required or used by FlyBase. The package set to use is taken from install.conf.local lines: #n packages to install PACKAGES = "argos-root flybase gmod" with related lines for apache, tomcat server instances, port numbers, etc. These lines are used to configure apache.conf to say which virtual host packages to enable. #n Includes for ROOT/conf/apache.conf - commented out directives by default #n To enable a web service, edit out the '#XXX_CONF' part FLYBASE_CONF = EUGENES_CONF = #EUGENES_CONF DAPHNIA_CONF = #DAPHNIA_CONF CENTAURBASE_CONF = #CENTAURBASE_CONF GMOD_CONF = Then step (4) uses information in the install/ files to proceed with fetching all the data, software, etc. for packages you've identified. | Second problem: flybase installation: the installation kicks off directories are | created, but the rsync always hangs on the /flybase/data transfer Ê(i left it | there for 12 hrs to see if it would continue). To overcome this problem I run | the installation interactively and hit a ctrl C, when it appears no more files | are being transferred, the flybasse/indices installation then starts. This sounds like the same problem Delwood ran into, related I think to firewall or other issues between novartis and flybase.net. We do have the same files available by anonymous ftp. This install software isn't yet able to use ftp (issues are with data updates mostly, as ftp lacks those updating abilities that rsync has). It is on my list of things todo to add ftp as alternate to rsync (probably using wget client). Probably what would work is for you to do the first install of bulk data with ftp "by hand", then updating changes by rsync won't be as big of a file set, and may not run into firewall problems. It is important for updating to preserve file dates, something that FTP doesn't always provide -- it depends on your client. The file install/packages.conf identifies parts and URL's for installing the primary packages. There are a few sub-packages for argos-root, several for flybase. See components at the bottom of page http://flybase.net:8081/install/install.cgi Main packages to install: Package Local path Disk use Description Requires argos-root 50 Mb Argos root server package argos-root argos-common flybase flybase/ 4 GB FlyBase Next Generation server package flybase argos-common flybase-data flybase-indices flybase-genomes flybase-blast bionet-drosophila gmod gmod/ 50 Mb sample GMOD database install gmod argos-common argos-root For flybase package these are component URLs from install/packages.conf, where an ftp fetch, starting from directory /bio/argos/ or your base folder, would be like this: ftp {alt-url-ftp} {localpath} Using wget software, this should work. Remove flags -q (quiet) and -b (background) if you want to see all the fetches on console. Note: I haven't tested this fully. It will fetch some extra files that are excluded from rsync packages, and it may overwrite needed files (e.g. common/system-local symlink). cd /bio/argos/ # package: argos-common wget -m ftp://flybase.net/argos/common/ \ --directory-prefix=common/ \ --cut-dirs=2 -nH -q -b # package: flybase wget -m ftp://flybase.net/argos/flybase/ \ --directory-prefix=flybase/ \ --cut-dirs=2 -nH -q -b # package: flybase-data wget -m ftp://flybase.net/flybase/ \ --directory-prefix=flybase/data/ \ --cut-dirs=1 -nH -q -b # package: flybase-indices - above flybase gets these without exclude:indices # package: flybase-dmel-genome wget -m ftp://flybase.net/genomes/Drosophila_melanogaster/current/ \ --directory-prefix=flybase/data/genomes/Drosophila_melanogaster/current/ \ --cut-dirs=3 -nH -q -b # package: flybase-dmel-hetchr wget -m ftp://flybase.net/genomes/Drosophila_melanogaster/current_hetchr/ \ --directory-prefix=flybase/data/genomes/Drosophila_melanogaster/current_hetchr/ \ --cut-dirs=3 -nH -q -b # package: flybase-dpse-genome wget -m ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/ \ --directory-prefix=flybase/data/genomes/Drosophila_pseudoobscura/current/ \ --cut-dirs=3 -nH -q -b # package: flybase-dmel-blast_misc wget -m ftp://flybase.net/genomes/Drosophila_melanogaster/blast_misc/ \ --directory-prefix=flybase/indices/blastsets/dmel_misc/ \ --cut-dirs=3 -nH -q -b # package: flybase-dpse-blast_misc wget -m ftp://flybase.net/genomes/Drosophila_pseudoobscura/blast_misc/ \ --directory-prefix=flybase/indices/blastsets/dpse_misc/ \ --cut-dirs=3 -nH -q -b # package: bionet-drosophila wget -m ftp://flybase.net/usenet/bionet/drosophila/ \ --directory-prefix=flybase/usenet/bionet/drosophila/ \ --cut-dirs=3 -nH -q -b ------ 1. Download: installargos.pl Also please read Readme-current.txt and argos-system-management.txt 2. Bootstrap installation: From command line, Run (change /bio/argos as desired) 'perl installargos.pl -root=/bio/argos -install -v' 3. Configure: Check desired packages below, edit Installation path, and press Configure button Installation path: 4. Install full data, software set: Run 'cd /bio/argos; install/install -install -v' This can take a while, use 'install/install -install -v >& log.install &' for background 5. Check installation, Start web server, Check logs/: Run 'install/run-apache start' The Argos web server should then be available at http://localhost:8081/ with installed packages at configured ports (status in logs/) 6. Update regularly: Run 'install/install -update [-v -n] [-rsopts=-v,-n]' See this example entry for server management.