Difference between revisions of "Building Frozen Releases"

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Line 9: Line 9:
 
* Debian "Lenny"
 
* Debian "Lenny"
  
−
=Server Configuration =
+
=General Server Configuration =
  
 
All WormBase-specific files are maintained in a shared directory.
 
All WormBase-specific files are maintained in a shared directory.
Line 21: Line 21:
 
     ...
 
     ...
  
−
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:
+
Each frozen release is a separate name-based VirtualHost.  To prevent collision of libraries, version specific Perl modules are maintained in:
  
 
   /usr/local/wormbase/VERSION/extlib
 
   /usr/local/wormbase/VERSION/extlib
  
−
@INC is prepended with this path for each virtual host during apache launch.
+
@INC is prepended with this path using mod_perl2 "PerlSwitches" option described below.
  
 
== Users, groups, directories ==
 
== Users, groups, directories ==
Line 40: Line 40:
  
 
Note that EACH virtual host will need its own xinetd configuration file and unique port on which acedb will bind.
 
Note that EACH virtual host will need its own xinetd configuration file and unique port on which acedb will bind.
−
 
−
This port MUST correspond in the localdefs.pm file (discussed below).
 
−
 
−
WS100 ... 2005
 
−
WS110 ... 2006
 
−
WS120 ... 2007
 
−
WS130 ... 2008
 
−
WS140 ... 2009
 
−
WS150 ... 2010
 
−
WS160 ... 2011
 
−
WS170 ... 2012
 
−
WS180 ... 2013
 
−
WS190 ... 2014
 
−
WS200 ... 2015
 
  
 
Furthermore, the names of each service (acedb_WSXXX) and its port needs to correspond to the name of the service in /etc/services.
 
Furthermore, the names of each service (acedb_WSXXX) and its port needs to correspond to the name of the service in /etc/services.
Line 61: Line 47:
 
Install and configure MySQL as [[OICR-Configuring_the_development_machine#MySQL|previously described]].
 
Install and configure MySQL as [[OICR-Configuring_the_development_machine#MySQL|previously described]].
  
−
Each frozen release will have one or more database of the form species_VERSION or g_species_VERSION.  Give access to each of these for the www-data user:
+
== Apache2 and mod_perl2 ==
 +
 
 +
Install and configurate Apache2 and mod_perl2 as [[OICR-Configuring_the_development_machine#Apache2_and_mod_perl|described]].
 +
 
 +
= Establishing A New Frozen Release =
 +
 
 +
== Copy software and libraries ==
 +
 
 +
It is easiest to set up a new frozen release if you do this when the desired release still resides on the development machine.
 +
 
 +
$ cd /usr/local/wormbase
 +
$ rsync -Cav website-classic user@wb-dev2:/usr/local/wormbase
 +
$ ssh wb-dev2
 +
$ cd /usr/local/wormbase
 +
$ mv website-classic [VERSION]
 +
 
 +
== AceDB database ==
 +
 
 +
Copy the appropriate AceDB database to:
 +
 +
$ /usr/local/wormbase/acedb/wormbase_VERSION
 +
 
 +
== MySQL databases ==
 +
 
 +
Copy mysql databases to the mysql data dir (/var/lib/mysql).
 +
 
 +
Append the database version to each mysql database if it isn't already versioned:
 +
 
 +
    species_[VERSION] or g_species_[VERSION]
 +
 
 +
Give access to each of these for the www-data user:
  
 
  grant select on elegans_WS110.* to www-data@localhost;
 
  grant select on elegans_WS110.* to www-data@localhost;
  
−
== Apache2 and mod_perl2 ==
+
== Perl Libraries ==
 +
 
 +
If you rsync the website as decribed above, you shouldn't need to install Perl libraries.  If you do, use follow the basic instructions on [[Managing Perl Libraries]].
 +
 
 +
Invoke it as:
 +
 
 +
$ ./install_perl_libraries.sh /usr/local/wormbase/[VERSION]/extlib
 +
 
 +
Be sure to "rm -rf ~/.cpan" before beginning, as well as clearing your PERL5LIB environment variable.
 +
 
 +
== BioPerl and GBrowse ==
 +
 
 +
For releases < WS200, install BioPerl 1.6.0 and GBrowse 1.69.  This isn't  entirely historically accurate, but it avoids security holes in GBrowse < 1.69.
 +
 
 +
$ cd /usr/local/wormbase/build/bioperl-1.6.0
 +
$ perl ./Build.PL --install_base /usr/local/wormbase/VERSION/extlib
 +
$ ./Build install
 +
 
 +
$ cd /usr/local/wormbase/build/Generic-Genome-Browser-1.69
 +
$ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/VERSION/extlib
 +
$ make
 +
$ make install
  
−
Install and configurate Apache2 and mod_perl2 as [[OICR-Configuring_the_development_machine#Apache2_and_mod_perl|described]].
+
For releases > WS200, install GBrowse 1.70:
  
−
Each frozen release will warrant its own instance of apache.  To do this.
+
$ cd /usr/local/wormbase/build/Generic-Genome-Browser-1.70
 +
  $ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/VERSION/extlib
 +
$ make
 +
$ make install
  
−
Copy the apache configuration directory.
+
== Fix configuration files ==
  
−
  $ cd /etc
+
=== VirtualHost Configuration ===
−
  $ sudo cp -r apache2 apache2-WSXXX
 
  
−
Set up name based virtual hosts for each frozen release as follows:
+
Add an appropriate VirtualHost stanza for the frozen release to the apache2 configuration.
 
   
 
   
−
   $ cd /etc/sites-available/default
+
   $ sudo emacs /etc/apache2/sites-enabled/000-default
−
  $ sudo cp /etc/apache2-WSXXX/
 
  
 
   <VirtualHost *:80>
 
   <VirtualHost *:80>
Line 85: Line 123:
 
     ServerName ws[VERSION].wormbase.org
 
     ServerName ws[VERSION].wormbase.org
 
     UseCanonicalName on
 
     UseCanonicalName on
 +
    PerlOptions +Parent
 +
 
 +
    # Versions prior to WS204
 +
    PerlSwitches -Mlib=/usr/local/wormbase/VERSION/extlib \
 +
                -Mlib=/usr/local/wormbase/WS200/lib \
 +
                -Mlib=/usr/local/wormbase/WS200/cgi-perl/lib \
 +
                -Mlib=/usr/local/wormbase/VERSION/extlib/lib \
 +
                -Mlib=/usr/local/wormbase/VERSION/extlib/lib/perl5
 +
 +
    # Versions >= WS204 which used local::lib for library management 
 +
    PerlSwitches -Mlib=/usr/local/wormbase/website-classic/extlib/lib/perl5 \
 +
                -Mlib=/usr/local/wormbase/website-classic/extlib/lib/perl5/x86_64-linux-gnu-thread-multi
 +
 +
    PerlInterpStart 2
 +
    PerlInterpMax 2
 
   </VirtualHost>
 
   </VirtualHost>
  
 
Be certain to remove or comment out the default configuration.
 
Be certain to remove or comment out the default configuration.
  
−
To launch apache2:
 
  
−
== Fetch frozen releases and unpack ==
+
=== xinetd.d/acedb_[WSVERSION] ===
  
−
$ ssh brie4
+
Create an xinetd.d/acedb_WSVERSION file for the server. The server port and path should correspond to one of the following:
−
$ 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/
+
WS100 ... 2005
−
* Unpack GFF databases into /var/lib/mysql/
+
WS110 ... 2006
−
* Prepend the version onto each mysql database: species_VERSION or g_species_VERSION
+
WS120 ... 2007
 +
WS130 ... 2008
 +
WS140 ... 2009
 +
WS150 ... 2010
 +
WS160 ... 2011
 +
WS170 ... 2012
 +
WS180 ... 2013
 +
WS190 ... 2014
 +
WS200 ... 2015
 +
WS204 ... 2016
 +
WS205 ... 2017
  
−
WHERE DO THE BLAST/BLAT DATABASES GO?
+
''Please keep this list up-to-date when establishing a new frozen release.''
  
−
== Perl Libraries ==
+
=== /etc/services ===
  
−
Each frozen release will rely on both a shared extlib (/usr/local/wormbase/extlib) as well as its OWN set of Perl libraries located at /usr/local/wormbase/VERSION/extlib.  I realize this is a little redundant but this is the best and easiest way to keep critical components like BioPerl and GBrowse distinct.
+
Add an entry in /etc/services for the corresponding service and port.
−
 
 
−
To do this, I've created separate CPAN configuration files for each release.  Unfortunately, I see no way to initialize a CPAN session with a unique configuration file on the command line.  This means they need to be manually swapped back and forth.  You also have to pay careful attention to initializing environment variables so CPAN can find the modules you may be building against.  It's a pain, I know.
 
−
 
 
−
Here's the general flow.
 
−
 
−
$ cp ~tharris/cpan_configuration/MyConfig.pm.WS100 ~/.cpan/CPAN/MyConfig.pm
 
−
$ export PERL5LIB=/usr/local/wormbase/WS100/extlib/lib:/usr/local/wormbase/WS100/extlib:/usr/local/wormbase/WS100/extlib/lib/perl5
 
−
 
 
−
You can accomplish the same thing by:
 
−
 
 
−
$ ~tharris/swap_cpan_configuration VERSION
 
−
 
 
−
Note: You may need to either make clean when using CPAN or delete .cpan/build before trying to build libraries for a new frozen release.
 
−
 
 
−
== Fix configuration files ==
 
  
 
=== perl.startup ===
 
=== perl.startup ===
  
 +
* /usr/local/wormbase/[VERSION]/conf/perl.startup
 
* Insert the VERSION into all appropriate "use lib" statements.
 
* Insert the VERSION into all appropriate "use lib" statements.
 
* Add "use Apache2::compat" for mod_perl1 backwards compatability.
 
* Add "use Apache2::compat" for mod_perl1 backwards compatability.
Line 130: Line 175:
 
=== httpd.conf ===
 
=== httpd.conf ===
  
 +
* /usr/local/wormbase/[VERSION]/conf/httpd.conf
 
* Change all occurrences of /usr/local/wormbase to /usr/local/wormbase/VERSION
 
* Change all occurrences of /usr/local/wormbase to /usr/local/wormbase/VERSION
 
* Change the ServerName as appropriate
 
* Change the ServerName as appropriate
Line 136: Line 182:
 
* In the "Location /db/" stanza, replace the PerlHandler line with:
 
* In the "Location /db/" stanza, replace the PerlHandler line with:
 
   PerlResponseHandler  ModPerl::Registry
 
   PerlResponseHandler  ModPerl::Registry
 +
* Edit the PerlRequire so that perl.startup is brought in AFTER configuration:
 +
  PerlPostConfigRequire /usr/local/wormbase/VERSION/conf/perl.startu
  
 
=== elegans.pm ===
 
=== elegans.pm ===
  
−
* Update the WS200 variable
+
* /usr/local/wormbase/[VERSION]/conf/elegans.pm
 +
* Change the path to our root: /usr/local/wormbase/VERSION
 
* Change the symbolic name of the acedb database to wormbase_VERSION
 
* Change the symbolic name of the acedb database to wormbase_VERSION
 
* Append the version to all GFF databases
 
* Append the version to all GFF databases
Line 145: Line 194:
 
=== gbrowse.conf ===
 
=== gbrowse.conf ===
  
−
* Append the version to all GFF databases
+
* /usr/local/wormbase/[VERSION]/conf/gbrowse.conf/*.conf
 +
* Append the version to all GFF database conf files (conf/gbrowse.conf/*.conf).
 +
 
 +
=== Apache/AddWormBaseBanner.pm ===
 +
 
 +
* /usr/local/wormbase/[VERSION]/lib/Apache/AddWormBaseBanner.pm
 +
 
 +
The mod_perl handler resposible for adding headers and footers needs to be fixed so that it can correctly redirect / request to /index.html.  See [http://www.wormbase.org/wiki/index.php/WormBase_Development_Environment#Important_Fix_for_mod_perl2.2Fmod_dir_incompatibility_.28the_index.html_problem.29 here] for details.
 +
 
 +
== Static Files ==
 +
 
 +
Copy appropriate static files to /usr/local/wormbase/data_freezes.  See the existing contents for examples.
 +
 
 +
== Support Databases ==
 +
 
 +
Copy the [VERSION] support databases file to
 +
 
 +
/usr/local/wormbase/databases/.
 +
 
 +
= Migrating Frozen Releases =
 +
 
 +
== 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?
 +
 
 +
Follow the configuration directives above as described for establishing a new frozen release.
 +
 
 +
= TODO =
 +
 
 +
* Install NCBI and WU-BLAST
 +
* Install BLAT and monitoring scripts; modify paths as req'd
 +
 
 +
* WS190 index.html is a new version and needs to be pulled from the VMX
 +
* WS180 index.html is a new version and needs to be pulled from the VMX
 +
* WS170 index.html is a new version and needs to be pulled from the VMX
 +
* WS160 index.html is a new version and needs to be pulled from the VMX
 +
* WS100: modules, Ace, GBrowse, enable system config, local config, missing files!
 +
 
 +
 
 +
[[Category: Maintenance (Web Dev)]]
 +
[[Category:Developer documentation]]

Latest revision as of 17:35, 19 June 2014

Hardware

WormBase frozen releases are hosted on the virtualized server:

wb-dev2.oicr.on.ca

  • 500 GB disk space
  • 4 GB RAM
  • Debian "Lenny"

General 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 name-based VirtualHost. To prevent collision of libraries, version specific Perl modules are maintained in: 

  /usr/local/wormbase/VERSION/extlib

@INC is prepended with this path using mod_perl2 "PerlSwitches" option described below.

Users, groups, directories

Set up the basic users, groups, and directories as previously described.

Installing system libraries

Prepare the system by installing a slew of libraries.

AceDB

Build AceDB as previously described.

Note that EACH virtual host will need its own xinetd configuration file and unique port on which acedb will bind.

Furthermore, the names of each service (acedb_WSXXX) and its port needs to correspond to the name of the service in /etc/services.

MySQL

Install and configure MySQL as previously described.

Apache2 and mod_perl2

Install and configurate Apache2 and mod_perl2 as described.

Establishing A New Frozen Release

Copy software and libraries

It is easiest to set up a new frozen release if you do this when the desired release still resides on the development machine. 

$ cd /usr/local/wormbase
$ rsync -Cav website-classic user@wb-dev2:/usr/local/wormbase
$ ssh wb-dev2
$ cd /usr/local/wormbase
$ mv website-classic [VERSION]

AceDB database

Copy the appropriate AceDB database to: 

$ /usr/local/wormbase/acedb/wormbase_VERSION

MySQL databases

Copy mysql databases to the mysql data dir (/var/lib/mysql).

Append the database version to each mysql database if it isn't already versioned: 

   species_[VERSION] or g_species_[VERSION]

Give access to each of these for the www-data user: 

grant select on elegans_WS110.* to www-data@localhost;

Perl Libraries

If you rsync the website as decribed above, you shouldn't need to install Perl libraries. If you do, use follow the basic instructions on Managing Perl Libraries.

Invoke it as: 

$ ./install_perl_libraries.sh /usr/local/wormbase/[VERSION]/extlib

Be sure to "rm -rf ~/.cpan" before beginning, as well as clearing your PERL5LIB environment variable.

BioPerl and GBrowse

For releases < WS200, install BioPerl 1.6.0 and GBrowse 1.69. This isn't entirely historically accurate, but it avoids security holes in GBrowse < 1.69. 

$ cd /usr/local/wormbase/build/bioperl-1.6.0
$ perl ./Build.PL --install_base /usr/local/wormbase/VERSION/extlib
$ ./Build install

$ cd /usr/local/wormbase/build/Generic-Genome-Browser-1.69
$ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/VERSION/extlib
$ make
$ make install

For releases > WS200, install GBrowse 1.70: 

$ cd /usr/local/wormbase/build/Generic-Genome-Browser-1.70
$ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/VERSION/extlib
$ make
$ make install

Fix configuration files

VirtualHost Configuration

Add an appropriate VirtualHost stanza for the frozen release to the apache2 configuration. 

 $ sudo emacs /etc/apache2/sites-enabled/000-default

 <VirtualHost *:80>
   Include /usr/local/wormbase/VERSION/conf/httpd.conf
   ServerName ws[VERSION].wormbase.org
   UseCanonicalName on
   PerlOptions +Parent
 
   # Versions prior to WS204
   PerlSwitches -Mlib=/usr/local/wormbase/VERSION/extlib \
                -Mlib=/usr/local/wormbase/WS200/lib \
                -Mlib=/usr/local/wormbase/WS200/cgi-perl/lib \
                -Mlib=/usr/local/wormbase/VERSION/extlib/lib \
                -Mlib=/usr/local/wormbase/VERSION/extlib/lib/perl5

   # Versions >= WS204 which used local::lib for library management   
   PerlSwitches -Mlib=/usr/local/wormbase/website-classic/extlib/lib/perl5 \
                -Mlib=/usr/local/wormbase/website-classic/extlib/lib/perl5/x86_64-linux-gnu-thread-multi

   PerlInterpStart 2
   PerlInterpMax 2
 </VirtualHost>

Be certain to remove or comment out the default configuration.


xinetd.d/acedb_[WSVERSION]

Create an xinetd.d/acedb_WSVERSION file for the server. The server port and path should correspond to one of the following: 

WS100 ... 2005
WS110 ... 2006
WS120 ... 2007
WS130 ... 2008
WS140 ... 2009
WS150 ... 2010
WS160 ... 2011
WS170 ... 2012
WS180 ... 2013
WS190 ... 2014
WS200 ... 2015
WS204 ... 2016
WS205 ... 2017

Please keep this list up-to-date when establishing a new frozen release.

/etc/services

Add an entry in /etc/services for the corresponding service and port.

perl.startup

  • /usr/local/wormbase/[VERSION]/conf/perl.startup
  • Insert the VERSION into all appropriate "use lib" statements.
  • Add "use Apache2::compat" for mod_perl1 backwards compatability.

httpd.conf

  • /usr/local/wormbase/[VERSION]/conf/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
  • Edit the PerlRequire so that perl.startup is brought in AFTER configuration:
 PerlPostConfigRequire /usr/local/wormbase/VERSION/conf/perl.startu

elegans.pm

  • /usr/local/wormbase/[VERSION]/conf/elegans.pm
  • Change the path to our root: /usr/local/wormbase/VERSION
  • Change the symbolic name of the acedb database to wormbase_VERSION
  • Append the version to all GFF databases

gbrowse.conf

  • /usr/local/wormbase/[VERSION]/conf/gbrowse.conf/*.conf
  • Append the version to all GFF database conf files (conf/gbrowse.conf/*.conf).

Apache/AddWormBaseBanner.pm

  • /usr/local/wormbase/[VERSION]/lib/Apache/AddWormBaseBanner.pm

The mod_perl handler resposible for adding headers and footers needs to be fixed so that it can correctly redirect / request to /index.html. See here for details.

Static Files

Copy appropriate static files to /usr/local/wormbase/data_freezes. See the existing contents for examples.

Support Databases

Copy the [VERSION] support databases file to 

/usr/local/wormbase/databases/.

Migrating Frozen Releases

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?

Follow the configuration directives above as described for establishing a new frozen release.

TODO

  • Install NCBI and WU-BLAST
  • Install BLAT and monitoring scripts; modify paths as req'd
  • WS190 index.html is a new version and needs to be pulled from the VMX
  • WS180 index.html is a new version and needs to be pulled from the VMX
  • WS170 index.html is a new version and needs to be pulled from the VMX
  • WS160 index.html is a new version and needs to be pulled from the VMX
  • WS100: modules, Ace, GBrowse, enable system config, local config, missing files!
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