Difference between revisions of "Building Frozen Releases"
From WormBaseWiki
Jump to navigationJump to search| Line 15: | Line 15: | ||
ls /usr/local/wormbase | ls /usr/local/wormbase | ||
acedb/ | acedb/ | ||
| − | WS100 | + | logs/ // Cross-site logs |
| − | WS110 | + | WS100 // WS100 website |
| − | WS120 | + | WS110 // WS110 website |
| + | WS120 // WS120 website | ||
... | ... | ||
| Line 30: | Line 31: | ||
Please refer to [[OICR-Configuring_the_development_machine]] for details. | Please refer to [[OICR-Configuring_the_development_machine]] for details. | ||
| − | == Installing | + | == Installing system libraries == |
Assuming a vanilla Debian installation, install the following libaries via ''sudo apt-get install''. Some of these libraries are discussed below. | Assuming a vanilla Debian installation, install the following libaries via ''sudo apt-get install''. Some of these libraries are discussed below. | ||
| Line 57: | Line 58: | ||
$ screen | $ screen | ||
$ scp -r data_freezes wb-dev.oicr.on.ca:. | $ scp -r data_freezes wb-dev.oicr.on.ca:. | ||
| + | |||
| + | |||
| + | == 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 | ||
Revision as of 19:10, 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
$ ssh brie4 $ cd ~ftp/pub/wormbase $ screen $ scp -r data_freezes wb-dev.oicr.on.ca:.
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
