Difference between revisions of "Building Frozen Releases"
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byacc | byacc | ||
− | == Fetch frozen releases == | + | == Fetch frozen releases and unpack == |
$ ssh brie4 | $ ssh brie4 | ||
Line 59: | Line 59: | ||
$ scp -r data_freezes wb-dev.oicr.on.ca:. | $ scp -r data_freezes wb-dev.oicr.on.ca:. | ||
+ | * Unpack acedb_VERSION.ace.tgz or elegans_VERSION.ace.tgz into /usr/local/wormbase/acedb/ | ||
+ | * Unpack GFF databases into /var/lib/mysql/ | ||
+ | * Prepend the version onto each mysql database: species_VERSION or g_species_VERSION | ||
+ | |||
+ | WHERE DO THE BLAST/BLAT DATABASES GO? | ||
== Fix configuration files == | == Fix configuration files == |
Revision as of 19:15, 14 June 2009
Contents
Hardware
WormBase frozen releases are hosted on the virtualized server:
wb-dev2.oicr.on.ca
- 500 GB disk space
- 4 GB RAM
- Debian "Lenny"
Server Configuration
All WormBase-specific files are maintained in a shared directory.
ls /usr/local/wormbase acedb/ logs/ // Cross-site logs WS100 // WS100 website WS110 // WS110 website WS120 // WS120 website ...
Each frozen release is a separate virtual host running under a single Apache instance. To prevent collision of libraries, version specific Perl modules are maintained in:
/usr/local/wormbase/VERSION/extlib
@INC is prepended with this path for each virtual host during apache launch.
Users, groups, directories
Please refer to OICR-Configuring_the_development_machine for details.
Installing system libraries
Assuming a vanilla Debian installation, install the following libaries via sudo apt-get install. Some of these libraries are discussed below.
gcc curl wget bzip2 mysql-server mysql-server-5.0 libgd2-xpm-dev libgd2-xpm xinetd libdbd-mysql libdbd-mysql-perl apache2 libapache2-mod-perl2 libgtk2.0-0 libgtk2.0-dev libglib byacc
Fetch frozen releases and unpack
$ ssh brie4 $ cd ~ftp/pub/wormbase $ screen $ scp -r data_freezes wb-dev.oicr.on.ca:.
- Unpack acedb_VERSION.ace.tgz or elegans_VERSION.ace.tgz into /usr/local/wormbase/acedb/
- Unpack GFF databases into /var/lib/mysql/
- Prepend the version onto each mysql database: species_VERSION or g_species_VERSION
WHERE DO THE BLAST/BLAT DATABASES GO?
Fix configuration files
perl.startup
- Insert the VERSION into all appropriate "use lib" statements.
- Add "use Apache2::compat" for mod_perl1 backwards compatability.
httpd.conf
- Change all occurrences of /usr/local/wormbase to /usr/local/wormbase/VERSION
- Change the ServerName as appropriate
- Prepend the version to both the error and access logs
- Remove any unnecessary configuration (DAV, mailarch, etc)
- In the "Location /db/" stanza, replace the PerlHandler line with:
PerlResponseHandler ModPerl::Registry
elegans.pm
- Update the WS200 variable
- Change the symbolic name of the acedb database to wormbase_VERSION
- Append the version to all GFF databases
gbrowse.conf
- Append the version to all GFF databases