Difference between revisions of "OICR-Configuring the development machine"

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Line 21: Line 21:
 
   website-classic  // The classic WormBase website
 
   website-classic  // The classic WormBase website
 
   website  // The new-and-improved website!
 
   website  // The new-and-improved website!
 +
 +
== Installing Libraries ==
 +
 +
Assuming a vanilla Debian installation, install the following libaries and all of their dependencies 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
 +
      libreadline5-dev
 +
      flex
 +
      libdb4.6
 +
      libdb-dev
 +
      emacs
  
 
== Preparing directories and users ==
 
== Preparing directories and users ==
Line 26: Line 52:
 
WormBase uses several user accounts for directory and server permissions. You will need to create these users and several preliminary directories. Creating a new user and group varies among Unix flavors. On most Linux systems, the following commands will create the new groups. You should have sudo privilege to execute these commands.
 
WormBase uses several user accounts for directory and server permissions. You will need to create these users and several preliminary directories. Creating a new user and group varies among Unix flavors. On most Linux systems, the following commands will create the new groups. You should have sudo privilege to execute these commands.
  
−
== User and group accounts ==
+
=== User and group accounts ===
  
 
These users should not have a login password. They are to establish privileges only.
 
These users should not have a login password. They are to establish privileges only.
Line 60: Line 86:
 
  % groups
 
  % groups
  
−
== Directories ==
+
=== Directories ===
  
 
The root container for all things WormBase:
 
The root container for all things WormBase:
Line 118: Line 144:
 
You may ignore this step if you do not plan to mirror the WormBase FTP site. In the examples below, the -p option is used to create the intermediate parents of directories if they don't already exist. If your mkdir doesn't support this option, you will need to create the intermediate directories manually.
 
You may ignore this step if you do not plan to mirror the WormBase FTP site. In the examples below, the -p option is used to create the intermediate parents of directories if they don't already exist. If your mkdir doesn't support this option, you will need to create the intermediate directories manually.
  
−
== Install Perl modules ==
+
== Perl modules ==
 +
 
 +
=== CPAN / Environment configuration ===
 +
 
 +
I maintain a suite of Perl modules common to WormBase at:
 +
 
 +
  /usr/local/wormbase/extlib
  
−
NOTE:  It might be preferable to set up TWO seperate extlib directories, one for each site.  To do this, maybe I could set up multiple CPAN configuration files.
+
If you need to over-ride the default version of a module, place it in the extlib directory of either the classic or rearchitecure site:
  
−
''(Note: It might by necessary to install gcc, curl, wget, unzip, bzip2, etc via apt-get before beginning)''
+
  /usr/local/wormbase/website-classic/extlib
 +
    OR
 +
  /usr/local/wormbase/website/extlib
  
 
Set up CPAN to build modules in the local library path (/usr/local/wormbase/extlib):
 
Set up CPAN to build modules in the local library path (/usr/local/wormbase/extlib):
Line 131: Line 165:
 
For the Makefile.PL arguments, enter
 
For the Makefile.PL arguments, enter
 
   
 
   
−
   INSTALL_BASE=/usr/local/wormbase/extlib \
+
   INSTALL_BASE=/usr/local/wormbase/extlib
  
 
And for Build.PL enter
 
And for Build.PL enter
Line 146: Line 180:
 
   emacs ~/.bash_profile
 
   emacs ~/.bash_profile
 
   export PERL5LIB /usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib/lib/perl5
 
   export PERL5LIB /usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib/lib/perl5
 +
 +
=== Basic required modules ===
  
 
Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo..
 
Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo..
Line 151: Line 187:
 
  perl -I/usr/local/wormbase/extlib/lib -MCPAN -e shell
 
  perl -I/usr/local/wormbase/extlib/lib -MCPAN -e shell
  
−
<nowiki>
 
 
  YAML
 
  YAML
 
  LWP
 
  LWP
Line 161: Line 196:
 
  CGI::Session    // CPAN installation fails in local dirs; tries to install man3 in system path.
 
  CGI::Session    // CPAN installation fails in local dirs; tries to install man3 in system path.
 
  CGI::Cache
 
  CGI::Cache
 +
CGI::Toggle
 
  Date::Calc
 
  Date::Calc
 
  Date::Manip      // CPAN installation fails in local dirs; tries to install man3 in system path.
 
  Date::Manip      // CPAN installation fails in local dirs; tries to install man3 in system path.
−
 
−
--> Build and install Berkeley DB
 
−
    wget http://download.oracle.com/berkeley-db/db-4.7.25.tar.gz
 
−
    tar xzf db*
 
−
    cd db*
 
−
    cd build_unix
 
−
    ../dist/configure
 
−
    make
 
−
    sudo make install
 
−
 
 
  DB_File
 
  DB_File
 
  DBI
 
  DBI
 
  DBD::mysql  (mysql must be installed first)
 
  DBD::mysql  (mysql must be installed first)
 
  Digest::MD5
 
  Digest::MD5
−
  GD                 // 'sudo apt-get install libgd2-xpm-dev libgd2-xpm' first
+
  GD  
 
  GD::SVG
 
  GD::SVG
 
  GD::Graph
 
  GD::Graph
 +
GD::Graph::pie
 
  HTML::TokeParser
 
  HTML::TokeParser
 
  IO::Scalar
 
  IO::Scalar
Line 204: Line 231:
 
  XML::Twig
 
  XML::Twig
 
  XML::Simple
 
  XML::Simple
−
  </nowiki>
+
  Flickr::API
 +
Flickr::API::Simple (private)
 +
Log::Log4perl
 +
Bio::Graphics
 +
Data::Stag
 +
Class::Base
 +
 
 +
YAML LWP ExtUtils::MakeMaker Bundle::CPAN Cache::Cache Cache::FileCache CGI CGI::Session CGI::Cache CGI::Toggle Date::Calc Date::Manip DB_File DBI Digest::MD5 GD  GD::SVG GD::Graph GD::Graph::pie HTML::TokeParser IO::Scalar IO::String Image::GD::Thumbnail MIME::Lite Net::FTP Proc::Simple readline Search::Indexer SOAP::Lite Statistics::OLS Storable SVG SVG::Graph Test::Pod Text::Shellwords Time::Format WeakRef XML::SAX XML::Parser XML::DOM XML::Writer XML::Twig XML::Simple Flickr::API Log::Log4perl Bio::Graphics Data::Stag Class::Base
 +
 
 +
*  Note that even with INSTALL_BASE and install_base set for EUMM/MB, installation of some modules into local non-privileged paths will FAIL.  This is almost always due to an attempt to install man pages in system paths not using one of the INSTALL* paths.  The only solution with these modules is to install them by hand...
 +
 
 +
=== Ace.pm (for the Classic WormBase site) ===
 +
 
 +
Ace.pm provides programmatic access to Acedb. You can install it via CPAN:
 +
 
 +
  cpan> install Ace
 +
 
 +
During configuration, choose option (3), then set the remaining variables as follows:
 +
 
 +
  Site-specific configuration files:  /usr/local/wormbase/website-classic/conf
 +
                            CGI path:  /usr/local/wormbase/website-classic/cgi-bin
 +
                          HTML path:  /usr/local/wormbase/website-classic/html
 +
 
 +
=== BioPerl ===
 +
 
 +
Check out bioperl-live from my developer account:
 +
 
 +
  $ cd /usr/local/wormbase/build
 +
  $ svn co svn+ssh://USERNAME@dev.open-bio.org/home/svn-repositories/bioperl/bioperl-live/trunk bioperl-live
 +
  $ mv bioperl-live bioperl-live-tharris
 +
  $ cd bioperl-live-tharris
 +
  $ perl ./Build.PL install_base /usr/local/wormbase/extlib
 +
  $ ./Build test
 +
  $ ./Build install
  
 
=== Installing additional Perl modules ===
 
=== Installing additional Perl modules ===
  
−
NOTE: To install any additional Perl modules later make sure that:
+
To install Perl modules that are not included on this list (or are new dependencies):
  
 
1. Your CPAN is configured to install to /usr/local/wormbase/extlib
 
1. Your CPAN is configured to install to /usr/local/wormbase/extlib
Line 222: Line 282:
 
   perl Make.PL INSTALL_BASE=/usr/local/wormbase/extlib
 
   perl Make.PL INSTALL_BASE=/usr/local/wormbase/extlib
  
−
== Build ePCR NOT DONE ==
 
  
−
* e-PCR (modified version, required for e-PCR search page)
 
  
−
This is located in the directory /usr/local/wormbase/e-PCR, which will come into existence after the WormBase site update program wb_update_wormbase.pl has been successfully run (see [[HowTo_Build_A_WormBase_Mirror#Using_wb_update_wormbase.pl_to_update_the_installation|below]] for details). Once the directory has been generated, run:
+
== Generic Genome Browser ==
 +
 
 +
GBrowse 2.x
 +
 
 +
$ cd /usr/local/wormbase/build
 +
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
 +
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co Generic-Genome-Browser
 +
 
 +
$ mv Generic-Genome-Browser Generic-Genome-Browser-head-anonymous
 +
$ ln -s Generic-Genome-Browser-head-anonymous development-Generic-Genome-Browser
 +
$ perl ./Build.PL --install_base /usr/local/wormbase/extlib
 +
 
 +
$ ./Build reconfig
 +
NOTE: Run ./Build reconfig to change existing configuration.
 +
Reuse previous configuration as defaults? [y ]
 +
 
 +
**Beginning interactive configuration**
 +
Directory for GBrowse's config and support files? [/usr/local/wormbase/website-classic/conf/gb2]
 +
 
 +
    // DO NOT CHANGE: CGI::Toggle has hard-coded paths
 +
Directory for GBrowse's static images & HTML files? [/usr/local/wormbase/website-classic/html/gbrowse2]
 +
Directory for GBrowse's temporary data [/usr/local/wormbase/tmp/gbrowse2]
 +
Directory for GBrowse's example databases [/usr/local/wormbase/website-classic/html/gbrowse2]
 +
Apache CGI scripts directory? [/usr/local/wormbase/website-classic/cgi-perl/seq]    // Will automatically create a gb2/ subdirectory
 +
Internet port to run demo web site on (for demo)? [8000]
 +
Apache loadable module directory (for demo)? [/usr/lib/apache2/modules]
 +
User account under which Apache daemon runs? [www-data]
 +
Automatically update Apache config files to run GBrowse? [y] n
 +
 
 +
This will install all the GBrowse libraries into my shared library path. This might not be optimal...
 +
 
 +
  $ ./Build test
 +
  $ ./Build install
 +
 
 +
<pre>
 +
[tharris@wb-dev: GBrowse-1.988-2nGezp]> ./Build apache_conf
 +
NOTE: Run ./Build reconfig to change existing configuration.
 +
 
 +
INSTRUCTIONS: Paste the following into your Apache configuration
 +
file. You may wish to save it separately and include it using the
 +
Apache "Include /path/to/file" directive. Then restart Apache and
 +
point your browser to http://your.site/gb2/ to start browsing the
 +
sample genomes.
  
−
    $ cd /usr/local/wormbase/e-PCR
+
>>>>>> cut here <<<<<
−
    # Edit 'makefile' to run install rather than ginstall, which doesn't exist on Fedora Linux
+
Alias        "/gb2/i/" "/var/tmp/gbrowse2/images/"
−
    $ make
+
Alias        "/gb2"    "/usr/local/wormbase/website-classic/html/gb2"
−
    $ make install  # or just run 'install e-PCR /usr/local/bin'
+
ScriptAlias  "/gb2"      "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
  
−
The file /usr/local/wormbase/e-PCR/README-Wormbase describes the changes that were made to the original e-PCR distribution.
+
<Directory "/usr/local/wormbase/website-classic/html/gb2">
 +
  Options -Indexes -MultiViews +FollowSymLinks
 +
</Directory>
  
−
== Installing AceDB from a binary package ==
+
<Directory "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2">
 +
  SetEnv PERL5LIB "/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5"
 +
  SetEnv GBROWSE_CONF  "/usr/local/wormbase/website-classic/conf/gb2"
 +
</Directory>
  
−
$ cd /usr/local/wormbase/acedb/src
 
−
$ curl -O ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/ACEDB-binaryLINUX_4.4.9.39.tar.gz
 
−
$ curl -O ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/ACEDB-serverLINUX_4.4.9.39.tar.gz
 
−
$ cd ../ ; mkdir bin-4.9.39
 
−
$ ln -s bin-4.9.39 bin ; cd bin
 
−
$ tar xzf ../src/ACEDB*
 
  
−
Make sure that these files are executable and owned by root:
+
<IfModule mod_fastcgi.c>
 +
  Alias /fgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
 +
  <Location /fgb2>
 +
    SetHandler  fastcgi-script
 +
  </Location>
 +
  FastCgiConfig -initial-env PERL5LIB=/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5 -initial-env GBROWSE_CONF=/usr/local/wormbase/website-classic/conf/gb2
 +
</IfModule>
  
−
   $ chown root:root ~acedb/bin/*      # This sets both owner and group to 'root'.
+
<IfModule mod_perl.c>
 +
  Alias /mgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
 +
  PerlSwitches -I/usr/local/wormbase/extlib/lib -I/usr/local/wormbase/extlib -I/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi -I/usr/local/wormbase/extlib/lib/perl5
 +
   <Location /mgb2>
 +
    SetHandler perl-script
 +
    PerlResponseHandler ModPerl::Registry
 +
    PerlOptions +ParseHeaders
 +
  </Location>
 +
</IfModule>
 +
</pre>
  
−
== Installing Ace.pm (Classic WormBase site) ==
 
  
−
Ace.pm provides programmatic access to Acedb. You can install it via CPAN:
+
GBrowse 1.x stable
  
−
   cpan> install Ace
+
   $ cd /usr/local/wormbase/build
 +
  $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
 +
  $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r stable Generic-Genome-Browser
 +
  $ ln -s Generic-Genome-Browser-stable-anonymous
 +
  $ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib
 +
    Apache root directory (enter '' for none)?
 +
    Apache conf directory? [/etc/apache2] /usr/local/wormbase/website-classic/conf
 +
    Apache htdocs directory? [/var/www] /usr/local/wormbase/website-classic/html
 +
    Apache cgibin directory? [/usr/lib/cgi-bin] /usr/local/wormbase/website-classic/cgi-perl/seq
 +
    GBrowse root for static files? [gbrowse] gbrowse
  
−
During configuration, choose option (3), then set the remaining variables as follows:
+
== AceDB ==
  
−
  Site-specific configuration files:  /usr/local/wormbase/website-classic/conf
+
I always build acedb from source.
−
                            CGI path:  /usr/local/wormbase/website-classic/cgi-bin
 
−
                          HTML path:  /usr/local/wormbase/website-classic/html
 
  
−
== Installing BioPerl NOT DONE ==
+
$ tar xzf ACEDB-source*    // CAUTION: Tarbomb.
 +
// Requires installation of a whole bunch of things first: libgtk2.0-0 libgtk2.0-dev libglib, byacc, etc, etc
 +
// Modify the makefile: create a target for server programs (xace tace saceserver sgifacerver)
 +
// This is all I care about:
 +
    SERVERS = xace tace saceserver sgifaceserver saceclient
 +
    servers: $(SERVERS)
 +
$ export ACEDB_MACHINE=LINUX_4
 +
$ make servers
 +
$ cd ~acedb
 +
$ ln -s bin-VERSION bin
 +
$ cp tace xace sgifaceserver saceserver saceclient ~acedb/bin/.
 +
$ sudo chown root:root ~acedb/bin/*
  
−
You may install BioPerl either using anonymous CVS or by downloading and installing the most recent stable core.
+
=== Testing the Installation ===
  
−
To install BioPerl from the current stable release (which was once recommended):  
+
At this point, you can test whether the socket server runs correctly. Provided that you have added yourself to the acedb group, you can run the following command:
  
−
% wget http://bioperl.org/DIST/current_core_stable.tar.gz
+
  % ~acedb/bin/sgifaceserver ~acedb/wormbase
−
% gunzip -c cur* | tar xvf -
+
  // Database directory: /usr/local/wormbase/acedb/wormbase
−
  % cd bioperl-1.4
+
  // Shared files: /usr/local/acedb
−
% perl Build.PL
+
  // #### Server started at 2001-07-23_16:42:31
−
  % ./Build test
+
  // #### host=mondseer.cshl.org listening port=23100
−
% sudo ./Build install
+
  // #### Database dir=/usr/local/acedb/elegans
 +
  // #### Working dir=/usr/local/acedb/elegans
 +
  // #### clientTimeout=600 serverTimeout=600 maxKbytes=0 autoSaveInterval=600
  
−
However, in March 2006 this stable release did not work with GBrowse-1.64. So the default choice is currently to install BioPerl from CVS. Installing from CVS will give you the latest version of BioPerl, but may also include unresolved bugs and experimental code.
+
  // Server listening socket 28 created
  
−
% cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login
+
The line "listening port=23100" indicates that the server is listening to port 23100. Open a new terminal window and use saceclient to confirm that you can communicate with the server:
−
    when prompted for the password, type 'cvs'
 
−
% cvs -d:pserver:cvs:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-live
 
−
% cd bioperl-live
 
−
% perl Build.PL
 
−
% ./Build test
 
−
% sudo ./Build install
 
−
 
  
−
(Note that BioPerl once used the old system of "perl Makefile.PL; make; make test; sudo make install", but that this has been superceded by the brave new world of Build.pm.)
+
% ~acedb/bin/saceclient localhost -port 23100
 +
Please enter userid: anonymous
 +
Please enter passwd:
 +
acedb@localhost&gt; find Sequence
 +
// Response: 65 bytes.
  
−
This will create a directory named bioperl-live. In the future, when you wish to update to the most recent version, simply type "cvs update" in the bioperl-live directory.  
+
// Found 236493 objects in this class
 +
// 236493 Active Objects
 +
acedb@localhost&gt; quit
 +
// Closing connection to server.
 +
// Client sent termination signal by server.
 +
// Response: 13 bytes.
 +
// A bientot
 +
// Please report problems to acedb@sanger.ac.uk
 +
// Bye
  
−
Install BioPerl in the usual way, by running "perl Makefile.PL", "make", "make test" and "make install".
+
=== Configuring Acedb to start automatically under xinetd ===
  
−
Finally, go into CPAN again and run:  
+
Install xinetd (not standard in Debian) if you didn't already:
  
−
cpan&gt; install Bio::Das
+
  $ sudo apt-get install xinetd
  
−
== Installing and configuring MySQL ==
+
Create a configuration file for acedb:
  
−
=== Installing MySQL ===
+
<nowiki>
 +
$ sudo emacs /etc/xinetd.d/acedb-wormbase
  
−
If working on a computer without pre-existing MySQL in its distribution, one can install from a binary distribution (without using a package manager). The commands are as follows (assuming an unpacked mysql distrbution!):
+
# file: /etc/xinetd.d/acedb-wormbase
−
 
+
# default: on
−
  $ wget http://mirror.trouble-free.net/mysql_mirror/Downloads/MySQL-5.1/mysql-5.1.35-linux-x86_64-glibc23.tar.gz
+
# description: wormbase acedb database
−
  $ groupadd mysql
+
service acedb
−
  $ useradd -g mysql mysql
+
{
−
  $ cd /usr/local
+
        protocol                = tcp
−
  $ sudo gunzip < /PATH/TO/MYSQL-VERSION-OS.tar.gz | tar xvf -
+
        socket_type            = stream
−
  $ sudo ln -s FULL-PATH-TO-MYSQL-VERSION-OS mysql
+
        port                    = 2005
−
  $ cd mysql
+
        flags                  = REUSE
−
  $ sudo scripts/mysql_install_db --user=mysql
+
        wait                    = yes
−
  $ sudo chown -R root .
+
        user                    = acedb
−
  $ sudo chown -R mysql data
+
        group                  = acedb
−
  $ chgrp -R mysql .
+
        log_on_success          += USERID DURATION
−
  $ bin/mysqld_safe --user=mysql &
+
        log_on_failure          += USERID HOST
 +
        server                  = /usr/local/wormbase/acedb/bin/sgifaceserver
 +
        server_args            = /usr/local/wormbase/acedb/wormbase 1200:1200:0
 +
}
 +
  </nowiki>
  
−
  # So the server starts up automatically, do:
+
Edit /etc/services. Although xinetd is not supposed to use /etc/services, the following line must be added:
−
  $ sudo cp support-files/mysql.server /etc/rc.d/init.d/mysql
 
−
  $ cd /etc/rc3.d
 
−
  $ sudo ln -s ../init.d/mysqld S99mysqld
 
−
  $ cd ../rc5.d
 
−
  $ sudo ln -s ../init.d/mysqld S99mysqld
 
  
−
  # Start the server by:
+
acedb-wormbase          2005/tcp
−
  $ sudo /etc/rc.d/init.d/mysql start
 
−
 
 
−
  # Set up a root password
 
−
  $ mysqladmin -uroot password PASSWORD
 
  
−
=== Set up mysql permissions ===
+
Restart xinetd with the following command:
  
−
  <nowiki># mysql -u root -pPASSWORD
+
  <nowiki># /etc/init.d/xinetd reload (or restart)
−
mysql> grant select on elegans.* to nobody@localhost;
 
 
  </nowiki>
 
  </nowiki>
  
−
  Repeat for: c_briggsae, c_japonica, c_remanei, c_brenneri, p_pacificus, b_malayi, c_elegans_gmap, c_elegans_pmap, autocomplete
+
You should now be able to talk to the database using saceclient:
 +
 
 +
% ~acedb/bin/saceclient localhost -port 2005
 +
 
 +
== MySQL ==
 +
 
 +
=== Installation ===
  
 +
Install mysql and various libraries via apt-get if you haven't already:
  
 +
  $ sudo apt-get install mysql-server-5.0 mysql-server libdbd-mysql libdbd-mysql-perl
  
 +
If it fails, then disable innodb by default. edit /etc/mysql/my.cnf file (uncomment the line):
  
 +
  #skip-innodb
 +
  $ sudo apt-get purge  mysql-server-5.0 mysql-server 
 +
  $ sudo apt-get install mysql-server-5.0 mysql-server
  
 +
With this installation, databases are located at '''/var/lib/mysql'''.  We want to able to write to this directory from the command line, so:
 +
 
 +
  $ sudo chmod 2775 /var/lib/mysql
  
−
== Installing Apache and mod_perl ==
+
Mysqld will automatically be setup to launch at server boot (rc3 and rc5) -- no need to mess with init scripts.
  
−
Unpack Apache and mod_perl into two side-by-side directories:
+
=== Set up mysql permissions ===
  
−
  drwxr-xr-x    8 tharris      4096 Jul 16 15:42 apache_1.3.32/
+
  <nowiki># mysql -u root -pPASSWORD
−
  drwxr-xr-x  24 tharris      4096 Jul 16 14:45 mod_perl-1.30/
+
mysql> grant select on elegans.* to nobody@localhost;
 +
  </nowiki>
  
−
Enter the mod_perl directory, and run this command:
+
Repeat for:  
 +
* c_briggsae
 +
* c_japonica
 +
* c_remanei
 +
* c_brenneri
 +
* p_pacificus
 +
* b_malayi
 +
* c_elegans_gmap
 +
* c_elegans_pmap
 +
* autocomplete
 +
* h_bacteriophora
  
−
    $ perl Makefile.PL DO_HTTPD=1 USE_APACI=1 EVERYTHING=1 \
+
== Apache2 and mod_perl ==
−
        APACHE_PREFIX=/usr/local/apache \
 
−
        APACI_ARGS='--enable-shared=info --enable-shared=status'
 
  
−
The primary installation site of WormBase also needs the proxy module and uses this configuration command.
+
=== Installation ===
  
−
    $ perl Makefile.PL DO_HTTPD=1 USE_APACI=1 EVERYTHING=1 \
+
sudo apt-get install apache2
−
        APACHE_PREFIX=/usr/local/apache \
+
  sudo apt-get install libapache2-mod-perl2
−
        APACI_ARGS='--enable-shared=info --enable-shared=status \
 
−
                    --enable-shared=proxy --enable-module=rewrite'
 
−
    $ make
 
−
    $ make test
 
−
    $ make install
 
  
−
This will install Apache into the directory /usr/local/apache.
+
=== Configuration ===
  
 +
We will set up WormBase to be a virtual host running on the default port 80.  Add the following configuration directives to /etc/apache2/sites-enabled/000-default:
  
−
Apache2
+
<VirtualHost *:80>
 +
    Include /usr/local/wormbase/website-classic/conf/httpd.conf
 +
    // ServerName dev.wormbase.org
 +
    // UseCanonicalName on
 +
</VirtualHost>
  
−
sudo apt-get install apache2
+
Be certain to remove or comment out the default configuration.
  
−
sudo apt-get install libapache2-mod-perl2
+
Modify /usr/local/wormbase/website-classic/conf/httpd.conf to match the new directory layout.
  
−
== Installing the Generic Genome Browser ==
+
'''TODO: I NEED TO ACCOUNT FOR OTHER VIRUTAL SERVERS RUNNING ON THE DEVELOPMENT SITE'''
  
−
This is a CGI script and some Perl modules that use Bio::DB::GFF and Bio::Graphics to create the main WormBase genome display. It lives at www.gmod.org. Like BioPerl, GBrowse can be installed via anonymous CVS or from the current stable release. As of June 2006, the current stable release (1.64) is the only one that actually works.
+
====Important Fix for mod_perl2/mod_dir incompatibility (the index.html problem) ====
  
−
  Via the latest stable release:
+
mod_perl2 intercepts Apache requests before any other modules. This means that for locations/directories configured with PerlHandlers that requests for dir or dir/ will NOT automatically redirect to the value of DirectoryIndex. To fix this problem, the lib/Apache/AddWormBaseBanner.pm needs to be modified:
−
    $ wget http://easynews.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.64.tar.gz
 
−
    $ gunzip -c Gene* | tar xvf -
 
  
−
CVS doesn't work yet (as of June 2006), but:
+
Insert the following:
  
−
  Via CVS:
+
# We need two additional modules:
−
    $ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
+
use Apache2::Const -compile => qw(DIR_MAGIC_TYPE OK DECLINED);
−
      (When prompted for a password for anonymous, simply press the Enter key.)
+
use Apache2::SubRequest;
−
    $ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co Generic-Genome-Browser
 
  
−
Note that: (1) version 1.64 is the latest stable release as of June 2006, but later versions will probably exist; (2) the clumsy "wget-longURL" command is a way of getting around Sourceforge's lack of easy, reliable URLs available to users for source-code packages.
+
sub handler {
 +
    my $r = shift;
 +
  # --> Copy and paste starting here...
 +
  # A directory request has content-type = httpd/unix directory                                                           
 +
  # we check that the uri ends in a slash, since only in that case                                           
 +
  # do we want to redirect, and finally to avoid redirect loops                                                                                     
 +
  # we only do this on the initial request.                                                                                               
 +
  # You must load Apache2::SubRequest in order to run internal_redirect                                                                                                       
 +
  if ($r->content_type eq 'httpd/unix-directory'
 +
      && $r->uri =~ '/$' && $r->is_initial_req ) {
 +
      #        print STDERR "Accepting Directory Request\n";                                                                                                         
 +
      # warn "internal request";                                                                                                                                                                              
 +
        $r->internal_redirect($r->uri . 'index.html');
 +
        return OK;
 +
    }
  
−
On a Linux distribution using SELinux security (such as Fedora Core 4), compilation will fail until SELinux is in some way circumvented. One way to do this is:
+
== Build ePCR NOT DONE ==
  
−
    $ setsebool -P httpd_disable_trans 1
+
* e-PCR (modified version, required for e-PCR search page)
−
    $ /usr/local/apache/bin/httpd restart
 
  
−
Then enter the unpacked directory or that fetched by CVS and run the following incantation to install it in the proper place for WormBase:
+
This is located in the directory /usr/local/wormbase/e-PCR, which will come into existence after the WormBase site update program wb_update_wormbase.pl has been successfully run (see [[HowTo_Build_A_WormBase_Mirror#Using_wb_update_wormbase.pl_to_update_the_installation|below]] for details). Once the directory has been generated, run:
  
−
     $ perl Makefile.PL HTDOCS=/usr/local/wormbase/html \
+
     $ cd /usr/local/wormbase/e-PCR
−
                  CGIBIN=/usr/local/wormbase/cgi-perl/seq \
+
    # Edit 'makefile' to run install rather than ginstall, which doesn't exist on Fedora Linux
−
                  CONF=/usr/local/wormbase/conf \
 
−
                  --SELINUX=1                            # disables SELinux
 
 
     $ make
 
     $ make
−
     $ make install
+
     $ make install   # or just run 'install e-PCR /usr/local/bin'
  
−
The long Makefile.PL incantation can be cut-and-pasted from this document into the command line. The last argument of Makefile.PL is only needed if SELinux exists on the system.
+
The file /usr/local/wormbase/e-PCR/README-Wormbase describes the changes that were made to the original e-PCR distribution.
  
 
== Installing BLAT ==
 
== Installing BLAT ==
Line 454: Line 619:
 
The important thing to note is that the databases directory is a symbolic link to /usr/local/wormbase/blast. This is where the update_wormbase.pl script (described in the next section) dumps its BLAST databases.
 
The important thing to note is that the databases directory is a symbolic link to /usr/local/wormbase/blast. This is where the update_wormbase.pl script (described in the next section) dumps its BLAST databases.
  
 +
== The WormBase Software ==
  
 +
Check out the WormBase software from CVS:
  
 +
  $ cd /usr/local/wormbase
 +
  $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository co wormbase-website
 +
  $ mv wormbase-website website-classic
  
−
 
+
=== Configure localsdef.pm ===
−
 
 
−
 
 
−
 
 
−
== Installing Analog and Report Magic (optional) ==
 
−
 
 
−
If you are running an offical mirror site or would like to analyze accesses to your server, you should also install Analog and ReportMagic. These software packages will be used to automatically analyze the access logs on a running basis.
 
−
 
 
−
Fetch analog:
 
−
 
 
−
% wget http://www.analog.cx/analog-6.0.tar.gz
 
−
% tar xzf analog-6.0.tar.gz
 
−
% cd analog-6.0
 
−
% make
 
−
% cd ../
 
−
 
 
−
(Note: sometimes wget of analog-6.0.tar.gz will hang. In that case, just use your Web browser to get the package onto your desktop computer, then scp it to your WormBase mirror computer.)
 
−
 
 
−
Copy analog to the primary WormBase root:
 
−
 
 
−
% cp -r analog-6.0 /usr/local/wormbase/util/log_analysis/.
 
−
 
 
−
Install Report Magic
 
−
 
 
−
% wget http://www.reportmagic.org/rmagic-2.21.tar.gz
 
−
% tar xzf rmagic-2.21.tar.gz
 
−
 
 
−
Edit Install.PL to place the report magic files in /usr/local/wormbase. Replace:
 
−
 
 
−
$DEST = '/usr/local/bin/rmagic-${VERSION}/';
 
−
with
 
−
$DEST = '/usr/local/wormbase/util/log_analysis/rmagic/';
 
−
 
 
−
<nowiki># And install...
 
−
% sudo perl Install.PL
 
−
</nowiki>
 
−
 
 
−
= Configuring the WormBase installation =
 
−
 
 
−
Although most files are delivered through the update mechanism, you will need to customize several files. Templates for each file are provided.
 
−
 
 
−
 
 
−
 
 
−
== Testing AceDB ==
 
−
 
 
−
At this point, you can test whether the socket server runs correctly. Provided that you have added yourself to the acedb group, you can run the following command:
 
−
 
 
−
  % ~acedb/bin/sgifaceserver ~acedb/elegans
 
−
  // Database directory: /usr/local/acedb/elegans
 
−
  // Shared files: /usr/local/acedb
 
−
  // #### Server started at 2001-07-23_16:42:31
 
−
  // #### host=mondseer.cshl.org  listening port=23100
 
−
  // #### Database dir=/usr/local/acedb/elegans
 
−
  // ####  Working dir=/usr/local/acedb/elegans
 
−
  // #### clientTimeout=600 serverTimeout=600 maxKbytes=0 autoSaveInterval=600
 
−
 
 
−
  // Server listening socket 28 created
 
−
 
 
−
The line "listening port=23100" indicates that the server is listening to port 23100. Open a new terminal window and use saceclient to confirm that you can communicate with the server:
 
−
 
 
−
% ~acedb/bin/saceclient localhost -port 23100
 
−
Please enter userid: anonymous
 
−
Please enter passwd:
 
−
acedb@localhost&gt; find Sequence
 
−
// Response: 65 bytes.
 
−
 
 
−
// Found 236493 objects in this class
 
−
// 236493 Active Objects
 
−
acedb@localhost&gt; quit
 
−
// Closing connection to server.
 
−
// Client sent termination signal by server.
 
−
// Response: 13 bytes.
 
−
// A bientot
 
−
// Please report problems to acedb@sanger.ac.uk
 
−
// Bye
 
−
 
 
−
The command-line syntax for saceclient is "saceclient &lt;host&gt; -port &lt;port&gt;". When prompted for the userid, enter "anonymous" and just hit return when prompted for a password. We then issued a "find Sequence" command to count the number of sequences in the database (a lot), and "quit" to terminate the connection.
 
−
 
 
−
Now test that the admin password works:
 
−
 
 
−
~acedb/bin/saceclient localhost -port 23100
 
−
Please enter userid: admin
 
−
Please enter passwd: ******
 
−
acedb@localhost&gt; shutdown now
 
−
// Client sending shutdown to server
 
−
// Client sent termination signal by server.
 
−
// Response: 87 bytes.
 
−
// 0 Active Objects
 
−
// Sorry, emergency shutdown of server now executing
 
−
// A bientot
 
−
// Please report problems to acedb@sanger.ac.uk
 
−
// Bye
 
−
 
 
−
When prompted for the userid, we entered "admin" and gave the correct password. The command "shutdown now" causes the server to exit. If we did not have administrative privileges, we would have gotten an "unknown command" error at this stage.
 
−
 
 
−
== Apache configuration - ~/wormbase/conf/httpd.conf vs. ~/apache/conf/httpd.conf ==
 
−
 
 
−
There are two httpd.conf files to contend with: one in the main directory for the Apache server (/usr/local/apache) and one in the site software for WormBase (/usr/local/wormbase). Getting the Apache configuration right entails getting various directives in these two files to properly mesh. Generally speaking, you want to set things up so any request specific for the WormBase site goes to /usr/local/'''wormbase'''/conf/httpd.conf, but also that any HTTP request meant for general purposes can still be handled by the main software and configurations at /usr/local/'''apache'''/conf/httpd.conf.
 
−
 
 
−
In the prototype file /usr/local/wormbase/conf/httpd.conf.template, you will find an Apache configuration file containing WormBase-specific definitions. These definitions will include:
 
−
 
 
−
    CustomLog    /usr/local/wormbase/logs/access_log combined_format
 
−
    &lt;Directory /usr/local/wormbase/html&gt; ... &lt;/Directory&gt;
 
−
    DocumentRoot /usr/local/wormbase/html
 
−
    ErrorLog    /usr/local/wormbase/logs/error_log
 
−
    LogFormat [various...]
 
−
    ServerAdmin webmaster@wormbase.org                        # change to your preferred e-mail address
 
−
 
 
−
These and other directives in /usr/local/wormbase/conf/httpd.conf will do the following:
 
−
 
 
−
# Set /usr/local/wormbase/html to be the document root for static HTML files.
 
−
# Set /usr/local/wormbase/db to be a script directory under the control of mod_perl's Apache::Registry.
 
−
# Create transfer and error logs in /usr/local/wormbase/logs
 
−
# Create an ordinary cgi-bin directory in /usr/local/wormbase/cgi-bin
 
−
# Put all static .html files under the control of Apache::AddWormbaseBanner, a module that appends the standard WormBase header and footer on all HTML files.
 
−
 
 
−
The simplest approach would be to cut-and-paste this file into the main configuration file (/usr/local/'''apache'''/conf/httpd.conf), replacing the directives already there. The approach recommended here, though, is to set up a WormBase-specific httpd.conf file:
 
−
 
 
−
    $ cp /usr/local/wormbase/conf/httpd.conf.template /usr/local/wormbase/conf/httpd.conf
 
−
 
 
−
Then use an Include directive in /usr/local/apache/conf/httpd.conf to import the WormBase-specific directives as needed. For instance, if WormBase is going to be the only website hosted by this server, then comment out all DocumentRoot and &lt;Directory&gt; sections, e.g.:
 
−
 
 
−
    #DocumentRoot "/usr/local/apache/htdocs"
 
−
 
 
−
from the main configuration file /usr/local/'''apache'''/conf/httpd.conf. Also, check that the Port directive in /usr/local/apache/conf/httpd.conf is "Port 80" (it should already be). Then, insert the following at the bottom of /usr/local/apache/conf/httpd.conf:
 
−
 
 
−
    Include /usr/local/'''wormbase'''/conf/httpd.conf
 
−
 
 
−
Conversely, if WormBase is going to be a virtual host (one of several web sites hosted by the server), then create an appropriate &lt;VirtualHost&gt; section in /usr/local/apache/conf/httpd.conf. Here is a template to follow:
 
−
 
 
−
    &lt;VirtualHost *:80&gt;
 
−
      ServerName wormbase.hostname.org                  # e.g., caltech.wormbase.org
 
−
      UseCanonicalName on
 
−
      Include /usr/local/wormbase/conf/httpd.conf
 
−
    &lt;/VirtualHost&gt;
 
−
 
 
−
    &lt;VirtualHost *:80&gt;
 
−
      ServerName your-non-wormbase.hostname.org
 
−
      UseCanonicalName on
 
−
      Include /usr/local/apache/conf/local_httpd.conf    # copy base configuration information to here
 
−
    &lt;/VirtualHost&gt;
 
−
 
 
−
For more details see the Apache documentation on [http://httpd.apache.org/docs/1.3/vhosts/ virtual hosts]. The IP address in the &lt;VirtualHost&gt; tag must be replaced by the correct IP address for the server. Likewise, the ServerName must be replaced by a DNS name that will correctly resolve to this IP address. N.B.: do not use "www.wormbase.org"! This name is already taken.
 
−
 
 
−
You must also set up a file for perl definitions:
 
−
 
 
−
    $ cp -p /usr/local/wormbase/conf/perl.startup.template /usr/local/wormbase/conf/perl.startup
 
−
 
 
−
However you end up applying it, /usr/local/wormbase/conf/httpd.conf needs a few small adjustments before use. First, change the filler name "your.machine.org" to the actual hostname of your server (or to an appropriate alias, such as "caltech.wormbase.org"); do this both for ServerName and at all other sites throughout the file. Likewise, change ServerAdmin to the e-mail address of whoever will actually be responsible for administering the mirror.
 
−
 
 
−
Also, update the location of the staging directory for dynamically-generated images to one suitable for your installation. This involves the following directive:
 
−
 
 
−
  Alias /ace_images  /var/tmp/ace_images
 
−
 
 
−
The ace_images directory will be created automatically the first time WormBase needs it, but the directory that it contains, in this case /var/tmp, must be writable by the Apache user (usually "nobody"). The images will eventually occupy approximately 10 megs. If /var/tmp is not appropriate for your system, change the second argument to some location that is more suitable.
 
−
 
 
−
== WormBase configuration - wormbase/conf/elegans.pm and localdefs.pm ==
 
−
 
 
−
=== elegans.pm ===
 
−
 
 
−
WormBase uses two main configuratation files, elegans.pm and localdefs.pm, located at /usr/local/wormbase/conf.
 
−
 
 
−
The first, elegans.pm, contains a variety of Perl definitions that are used by the various WormBase mod_perl scripts. You will want to look through this file, but you probably will not need to make any changes. The sole item you might wish to change controls the location of temporary files:
 
−
 
 
−
@PICTURES
 
−
 
 
−
This is the location of a temporary staging directory for dynamically-generated images as indicated in conf/httpd.conf. Its value is a list in which the first item is where the images will appear on the Web server (in URL space) and the second item is where they will appear on the filesystem:
 
−
 
 
−
  @PICTURES = ('/ace_images' =&gt; '/var/tmp/ace_images');
 
−
 
 
−
If you changed the location of the staging directory in httpd.conf, you must make the corresponding change here.
 
−
 
 
−
=== localsdef.pm ===
 
−
 
 
−
The second file, localdefs.pm, contains site-specific hostnames, ports, and passwords. You will find a template for this file at /usr/local/wormbase/conf/localdefs.pm.template. Copy this file to localdefs.pm and edit the following options as appropriate for your site.
 
  
 
* $HOST
 
* $HOST
Line 666: Line 662:
  
 
  $WORMBASE2BLAST=http://your.hostname.org/
 
  $WORMBASE2BLAST=http://your.hostname.org/
 +
 +
 +
 +
 +
 +
 +
  
 
== Configuring Servers To Start Automatically ==
 
== Configuring Servers To Start Automatically ==
Line 692: Line 695:
 
     10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
 
     10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
  
−
=== Configuring ACeDB to start automatically under inetd ===
 
  
−
Some, but not all, UNIX and Unix-like operating systems use inetd to automatically start background processes; in such a system, inetd must be configured to launch the acedb server. (Other systems such as Fedora Linux will use xinetd.)
 
  
−
Where inetd is used, locate the file /etc/inetd.conf, and add the following line to the end:
+
== Installing scripts to verify that the servers are running ==
  
−
    2005 stream tcp wait acedb /usr/local/acedb/bin/sgifaceserver sock.acedb /usr/local/acedb/elegans  1200:1200:0
+
Two scripts in the WormBase directory can be used to ensure that the mysql and blat servers are running. To install, them:
  
−
Note that this line may be wrapped into two or more lines when being viewed; but, in the real configuration file, this ''must'' be a single unbroken, unwrapped line. The first column indicates the port number to listen to. 2005 is the default used by the WormBase configuration files.
+
% sudo cp /usr/localwormbase/util/admin/blat_server.initd \
 +
          /etc/rc.d/init.d/blat_server
  
−
Tell inetd to reload its configuration file by sending it a HUP signal.
+
Place the restart scripts under cron control of a privileged user. These commands will check every hour to see that the servers are running.
  
−
    % ps -elf | grep inetd
+
  % sudo crontab -u root -e
−
    140 S root       500    1  0  60  0    -  329 do_sel Jul17¬†? inetd
 
−
    % killall -HUP 140
 
  
−
You should now be able to talk to the database using saceclient (as a anonymous user):
+
0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
 +
0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl
  
−
    % ~acedb/bin/saceclient localhost -port 2005
+
At the same time, you might also wish to automate the rotatation of logs to prevent them from growing to an unwieldy size. You'll find an appropriate log rotation configuration stanza in util/rotate_wormbase_logs and a log rotate script in /usr/local/wormbase/bin/rotatelogs.pl. You will need both.
  
−
=== Configuring Acedb to start automatically under xinetd ===
+
  <nowiki># Rotate httpd logs
−
 
+
  10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
−
First, make sure that xinetd is actually installed (look for the presence of /usr/sbin/xinetd). If not, use the RPM manager (gnorpm or equivalent) to install the xinetd package.
+
# Rotate acedb logs
−
 
+
10 1 * * * logrotate /usr/local/wormbase/util/rotate_wormbase_logs
−
Modern versions of xinetd (e.g., xinetd-2.3.13-6) distributed with Fedora Core 4 should work well. If for some reason you are using an old version (&lt;2.3.7), though, you must upgrade to at least xinetd-2.3.7-4.7x.
 
−
 
 
−
Once xinetd is installed, you will now need to create an xinetd configuration file for Acedb. Create a new file named /etc/xinetd.d/acedb with the following contents:
 
−
 
 
−
  <nowiki># file: /etc/xinetd.d/acedb
 
−
# default: on
 
−
# description: wormbase acedb database
 
−
service acedb
 
−
  {
 
−
        protocol                = tcp
 
−
        socket_type            = stream
 
−
        port                    = 2005
 
−
        flags                  = REUSE
 
−
        wait                    = yes
 
−
        user                    = acedb
 
−
        group                  = acedb
 
−
        log_on_success          += USERID DURATION
 
−
        log_on_failure          += USERID HOST
 
−
        server                  = /usr/local/acedb/bin/sgifaceserver
 
−
        server_args            = /usr/local/acedb/elegans 1200:1200:0
 
−
}
 
 
  </nowiki>
 
  </nowiki>
  
−
Edit /etc/services. Although xinetd is not supposed to use /etc/services, the following line must be added:
+
This stanza will check that the acedb server logs do not grow larger than 100 MB.
  
−
acedb          2005/tcp
 
  
−
Restart xinetd with the following command:
 
  
−
<nowiki># /etc/rc.d/init.d/xinetd reload (or restart)
 
−
</nowiki>
 
  
−
To kill xinetd, first find the process id and then:
 
−
 
−
<nowiki># kill -SIGUSR2 process#
 
−
</nowiki>
 
−
 
−
You should now be able to talk to the database using saceclient:
 
−
 
−
% ~acedb/bin/saceclient localhost -port 2005
 
−
 
−
Note: to know if the server is listening at port 2005, run the following command:
 
−
 
−
  # netstat -ant | grep LISTEN
 
−
  or, for more readable output,
 
−
  # netstat -vatp | grep LISTEN
 
−
 
−
If an error occurs, check /var/log/messages, and the serverlog.worm and log.wrm files in the current database directory. Common errors include insufficient disk space and inapprorpriate permissions for the latter two log files. Remember, the acedb server must be able to write to these files.
 
  
 
== Testing The Site ==
 
== Testing The Site ==
Line 772: Line 732:
  
 
  <nowiki># Via xinetd:
 
  <nowiki># Via xinetd:
−
  $ /etc/rc.d/init.d/xinetd reload (or restart)
+
  $ /etc/init.d/xinetd reload (or restart)
−
</nowiki>
 
−
 
 
−
<nowiki># Or to kill xinetd, first find the process id and then:
 
−
$ kill -SIGUSR2 process#
 
 
  </nowiki>
 
  </nowiki>
  
Line 785: Line 741:
 
  </nowiki>
 
  </nowiki>
  
−
=== MySQL ===
+
=== Restarting MySQL ===
  
 
  <nowiki># Via mysqladmin...
 
  <nowiki># Via mysqladmin...
Line 791: Line 747:
 
   
 
   
 
  # or using init.d
 
  # or using init.d
−
  $ /etc/rc.d/init.d/mysql restart
+
  $ /etc/init.d/mysql restart
 
  </nowiki>
 
  </nowiki>
  
−
=== Apache ===
+
=== Restarting Apache ===
  
 
When the configuration files have been checked and adjusted, restart Apache with the following command:
 
When the configuration files have been checked and adjusted, restart Apache with the following command:
  
−
   $ /usr/local/apache/bin/apachectl restart
+
   $ /etc/init.d/apache restart
  
−
Look in /usr/local/wormbase/logs/error_log (Wormbase-specific errors) and /usr/local/apache/logs/error_log (general errors) for any error messages. If there are none, try fetching the main page. You should see a WormBase banner and footer. The various database searches should also work.
+
Check /usr/local/wormbase/logs/classic-error_log for WormBase-specific errors and /var/log/apache2/error_log for general errors.
  
 
=== BLAT ===
 
=== BLAT ===
Line 814: Line 770:
 
     Disallow: /
 
     Disallow: /
  
−
= Troubleshooting =
+
=Updating Production Nodes to match this reality=
  
−
There are a number of common problems to check:
+
1. Create /usr/local/wormbase/website-classic
  
−
== Is the acedb socket server starting? ==
+
2. Move all website files into website-classic
  
−
Run "ps" to determine whether the server is indeed starting. If not, go back to the acedb configuration section and confirm that everything is where it should be. Make sure that the /usr/local/acedb/elegans/database directory is writable by the acedb user.
+
3. Move database to /usr/local/wormbase
  
−
The two acedb logs to check for error messages are both in /usr/local/acedb/elegans/database. Examine log.wrm and serverlog.wrm.
+
4. Create /usr/local/wormbase/logs
  
−
== Is the acedb socket server crashing? ==
+
5. Install Perl Modules as described above
  
−
It is possible that the server is crashing soon after it starts. The symptom of this is that the system gets very busy for a while, and "top" or "ps" shows the server restarting repeatedly. Eventually inetd (or xinetd) will disable the server and issue a syslog message to the effect that it is disabling a "looping" service.
+
6. Install GBrowse as described above
  
−
Again, check that acedb is installed properly and that the database directory is writable. Check log.wrm and serverlog.wrm.
+
7. Update admin module for pushing software to production (and for maintaining staging module)
  
−
== "Internal Server Error" ==
+
= AUTHOR =
  
−
This is typically a symptom that mod_perl isn't installed correctly, a required Perl library is missing, or something is wrong with the configuration. Check the two error_log files (in /usr/local/apache/log and /usr/local/wormbase/log) for clues.
+
[[User:Tharris|Todd Harris]]
  
−
== The banner displays but the decorative worm images are broken ==
 
  
−
On some versions of Linux running the libc 2.2 library there is a bug in readdir(), which is the function called to read the contents of a directory. You can check what version of glibc you have by looking at the contents of /lib:
 
−
 
−
% ls -l /libc-*
 
−
-rwxr-xr-x    1 root  root  4101324 Feb 29  2000 /lib/libc-2.1.3.so*
 
−
 
−
Versions that are at risk will show libc-2.2.so installed. The solution is to upgrade to a more recent version of libc. libc 2.2.3 is known to work correctly.
 
−
 
−
If you are stuck, send copies of the error logs and anything else you think might be useful to lstein@cshl.org and I'll try to help.
 
−
 
−
== Installing scripts to verify that the servers are running ==
 
−
 
−
Two scripts in the WormBase directory can be used to ensure that the mysql and blat servers are running. To install, them:
 
−
 
−
% sudo cp /usr/localwormbase/util/admin/blat_server.initd \
 
−
          /etc/rc.d/init.d/blat_server
 
−
 
−
Place the restart scripts under cron control of a privileged user. These commands will check every hour to see that the servers are running.
 
−
 
−
  % sudo crontab -u root -e
 
−
 
−
0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
 
−
0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl
 
−
 
−
At the same time, you might also wish to automate the rotatation of logs to prevent them from growing to an unwieldy size. You'll find an appropriate log rotation configuration stanza in util/rotate_wormbase_logs and a log rotate script in /usr/local/wormbase/bin/rotatelogs.pl. You will need both.
 
−
 
−
<nowiki># Rotate httpd logs
 
−
10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
 
−
# Rotate acedb logs
 
−
10 1 * * * logrotate /usr/local/wormbase/util/rotate_wormbase_logs
 
−
</nowiki>
 
−
 
−
This stanza will check that the acedb server logs do not grow larger than 100 MB.
 
−
 
−
== INSTALL libgd and GD.pm (if installation of GD.pm failed) ==
 
−
 
−
=== libgd ===
 
−
 
−
Try first to install it with the default package management system of yout distro/UNIX. If that fails you might want to resort to manual installation from source:
 
−
 
−
Fetch and install libgd:
 
−
 
−
  # curl -O http://www.boutell.com/gd/http/gd-2.0.33.tar.gz
 
−
  # tar xzf gd-2.0.33.tar.gz
 
−
  # cd gd-2.0.33
 
−
  # ./configure
 
−
  # make
 
−
  # sudo make install
 
−
 
−
=== GD.pm ===
 
−
 
−
try the usual cpan way, or:
 
−
 
−
  # curl -O http://stein.cshl.org/WWW/software/GD/GD.pm.tar.gz
 
−
  # tar xzf GD.pm.tar.gz
 
−
  # perl Makefile.PL -L/usr/local  // or export LD_LIBRARY_PATH=/usr/local
 
−
  # make
 
−
  # sudo make install
 
−
 
−
If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following:
 
−
 
−
  - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
 
−
    during execution
 
−
  - add LIBDIR to the `LD_RUN_PATH' environment variable
 
−
    during linking
 
−
  - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
 
−
  - have your system administrator add LIBDIR to `/etc/ld.so.conf'
 
−
 
−
DO I NEED TO REMOVE OLD VERSIONS OF GD FIRST?
 
−
 
−
  Finally reverted to 1.19!  Yikes!
 
−
  cpan&gt; install LDS/GD-1.19.tar.gz
 
−
 
−
== Install XML libraries and modules ==
 
−
 
−
The XML parsing libraries faciliate XML dumps from WormBase. They are not strictly required for a Wormbase installation.
 
−
 
−
=== expat ===
 
−
 
−
As with libgd, try to use your package manager, or:
 
−
 
−
  % curl -O http://umn.dl.sourceforge.net/sourceforge/expat/expat-1.95.6.tar.gz
 
−
  % gnutar -zxf expat-1.95.6.tar.gz
 
−
  % pushd expat-1.95.6/
 
−
  % ./configure
 
−
  % make
 
−
  % sudo make install
 
−
  % popd
 
−
 
−
 
−
 
−
= AUTHOR =
 
  
−
[[User:Tharris|Todd Harris]] (toddwharris@gmail.com)
+
[[Category:Developer documentation]]

Latest revision as of 19:55, 5 May 2022

Address

wb-dev.oicr.on.ca

Hardware

The WormBase development server at OICR is a virtual server with the following stats:

  • Debian Linux
  • 500 GB disk space (mounted at /dev/hda1)
  • 4 GB RAM

Server Configuration

All WormBase components are collected under a single directory: /usr/local/wormbase 

$ ls /usr/local/wormbase
  acedb/   // The Acedb database (including bin directory)
  util/    // Utility components such as e-pcr and wublast
  extlib/  // Third party Perl libraries   
  website-classic  // The classic WormBase website
  website  // The new-and-improved website!

Installing Libraries

Assuming a vanilla Debian installation, install the following libaries and all of their dependencies 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
     libreadline5-dev
     flex
     libdb4.6
     libdb-dev
     emacs

Preparing directories and users

WormBase uses several user accounts for directory and server permissions. You will need to create these users and several preliminary directories. Creating a new user and group varies among Unix flavors. On most Linux systems, the following commands will create the new groups. You should have sudo privilege to execute these commands.

User and group accounts

These users should not have a login password. They are to establish privileges only.

  • acedb group

This is the group that will have write privileges to the acedb directory tree. Acedb administrators should be added to this group. 

$ /usr/sbin/groupadd acedb
  • acedb user

This is the user that the acedb server will run as. It should be a member of the acedb group. 

$ /usr/sbin/useradd -g acedb -d /usr/local/wormbase/acedb acedb

This useradd command also adds the new acedb user to the acedb group. Note that the acedb user's home directory was set to /usr/local/acedb, a directory which will be created in the next step.

  • wormbase group

This is a group that will have write privileges to the wormbase directory tree. WormBase administrators and authors should be added to this group. 

$ /usr/sbin/groupadd wormbase

This would be a good time to add yourself to the acedb and wormbase groups. 

$ /usr/sbin/usermod -a -G acedb,wormbase [your_login_name]

[The '-a' argument keeps this command from deleting other, preexisting group memberships.]

You may need to re-login for these changes to take effect. Use the groups command to check which groups you are a member of: 

% groups

Directories

The root container for all things WormBase:

  • /usr/local/wormbase, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase
$ chgrp wormbase /usr/local/wormbase
$ chmod 2775 /usr/local/wormbase
  • External Perl libraries: /usr/local/wormbase/extlib, owner=tharris group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/extlib
$ chgrp wormbase /usr/local/wormbase/extlib
$ chmod 2775 /usr/local/wormbase/extlib
  • The "classic" website: /usr/local/wormbase/website-classic, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/website-classic
$ chgrp wormbase /usr/local/wormbase/website-classic
$ chmod 2775 /usr/local/wormbase/website-classic
  • /usr/local/wormbase/website-classic/logs, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/website-classic/logs
$ chgrp wormbase /usr/local/wormbase/website-classic/logs
$ chmod 2775 /usr/local/wormbase/website-classic/logs
  • /usr/local/wormbase/website-classic/cache, owner=nobody group=nobody mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/website-classic/cache
$ chown nobody:nobody /usr/local/wormbase/website-classic/cache
$ chmod 2775 /usr/local/wormbase/website-classic/cache
  • The "util" directory contains components that apply to both the classic and updated site, like wublast and e-pcr.
  • /usr/local/wormbase/util/wublast, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/util/wublast
$ chgrp wormbase /usr/local/wormbase/util/wublast
$ chmod 2775 /usr/local/wormbase/util/wublast
  • /usr/local/wormbase/acedb, owner=acedb group=acedb,mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/acedb
$ chown acedb:acedb /usr/local/wormbase/acedb
$ chmod 2775 /usr/local/wormbase/acedb

Configure the FTP/Mirroring directory THIS IS NOT DONE YET

  • ~ftp/pub/wormbase, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir ~ftp/pub/wormbase
$ chgrp wormbase ~ftp/pub/wormbase
$ chmod 2775 ~ftp/pub/wormbase

You may ignore this step if you do not plan to mirror the WormBase FTP site. In the examples below, the -p option is used to create the intermediate parents of directories if they don't already exist. If your mkdir doesn't support this option, you will need to create the intermediate directories manually.

Perl modules

CPAN / Environment configuration

I maintain a suite of Perl modules common to WormBase at: 

 /usr/local/wormbase/extlib

If you need to over-ride the default version of a module, place it in the extlib directory of either the classic or rearchitecure site: 

 /usr/local/wormbase/website-classic/extlib
   OR
 /usr/local/wormbase/website/extlib

Set up CPAN to build modules in the local library path (/usr/local/wormbase/extlib): 

 perl -MCPAN -e shell   // Note that you DO NOT need to be sudo...
 cpan> o conf init (only necessary if not prompted)

For the Makefile.PL arguments, enter 

 INSTALL_BASE=/usr/local/wormbase/extlib

And for Build.PL enter 

 --install_base /usr/local/wormbase/extlib

Prepare/update your CPAN: 

cpan> install CPAN
cpan> reload CPAN

Before installing modules, you may need to set your PERL5LIB environment variable to point to include the extlib directory. 

 emacs ~/.bash_profile
 export PERL5LIB /usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib/lib/perl5

Basic required modules

Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo.. 

perl -I/usr/local/wormbase/extlib/lib -MCPAN -e shell

YAML
LWP
ExtUtils::MakeMaker
Bundle::CPAN
Cache::Cache
Cache::FileCache
CGI
CGI::Session     // CPAN installation fails in local dirs; tries to install man3 in system path.
CGI::Cache
CGI::Toggle
Date::Calc
Date::Manip      // CPAN installation fails in local dirs; tries to install man3 in system path.
DB_File
DBI
DBD::mysql   (mysql must be installed first)
Digest::MD5
GD 
GD::SVG
GD::Graph
GD::Graph::pie
HTML::TokeParser
IO::Scalar
IO::String
Image::GD::Thumbnail
MIME::Lite
Net::FTP
Proc::Simple
readline
Search::Indexer
SOAP::Lite
Statistics::OLS
Storable
SVG
SVG::Graph
Test::Pod
Text::Shellwords
Time::Format
WeakRef
XML::SAX
XML::Parser
XML::DOM
XML::Writer
XML::Twig
XML::Simple
Flickr::API
Flickr::API::Simple (private)
Log::Log4perl
Bio::Graphics
Data::Stag
Class::Base

YAML LWP ExtUtils::MakeMaker Bundle::CPAN Cache::Cache Cache::FileCache CGI CGI::Session CGI::Cache CGI::Toggle Date::Calc Date::Manip DB_File DBI Digest::MD5 GD  GD::SVG GD::Graph GD::Graph::pie HTML::TokeParser IO::Scalar IO::String Image::GD::Thumbnail MIME::Lite Net::FTP Proc::Simple readline Search::Indexer SOAP::Lite Statistics::OLS Storable SVG SVG::Graph Test::Pod Text::Shellwords Time::Format WeakRef XML::SAX XML::Parser XML::DOM XML::Writer XML::Twig XML::Simple Flickr::API Log::Log4perl Bio::Graphics Data::Stag Class::Base
  • Note that even with INSTALL_BASE and install_base set for EUMM/MB, installation of some modules into local non-privileged paths will FAIL. This is almost always due to an attempt to install man pages in system paths not using one of the INSTALL* paths. The only solution with these modules is to install them by hand...

Ace.pm (for the Classic WormBase site)

Ace.pm provides programmatic access to Acedb. You can install it via CPAN: 

 cpan> install Ace

During configuration, choose option (3), then set the remaining variables as follows: 

 Site-specific configuration files:  /usr/local/wormbase/website-classic/conf
                           CGI path:  /usr/local/wormbase/website-classic/cgi-bin
                          HTML path:  /usr/local/wormbase/website-classic/html

BioPerl

Check out bioperl-live from my developer account: 

 $ cd /usr/local/wormbase/build
 $ svn co svn+ssh://USERNAME@dev.open-bio.org/home/svn-repositories/bioperl/bioperl-live/trunk bioperl-live
 $ mv bioperl-live bioperl-live-tharris
 $ cd bioperl-live-tharris
 $ perl ./Build.PL install_base /usr/local/wormbase/extlib
 $ ./Build test
 $ ./Build install

Installing additional Perl modules

To install Perl modules that are not included on this list (or are new dependencies):

1. Your CPAN is configured to install to /usr/local/wormbase/extlib

You can set this in ~/.cpan/CPAN/MyConfig.pm 

'makepl_arg' => q[INSTALL_BASE=/usr/local/wormbase/extlib],

OR

2. If building by hand, you call Makefile.PL as: 

  perl Make.PL INSTALL_BASE=/usr/local/wormbase/extlib


Generic Genome Browser

GBrowse 2.x 

$ cd /usr/local/wormbase/build
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co Generic-Genome-Browser

$ mv Generic-Genome-Browser Generic-Genome-Browser-head-anonymous
$ ln -s Generic-Genome-Browser-head-anonymous development-Generic-Genome-Browser
$ perl ./Build.PL --install_base /usr/local/wormbase/extlib

$ ./Build reconfig
NOTE: Run ./Build reconfig to change existing configuration.
Reuse previous configuration as defaults? [y ]

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/usr/local/wormbase/website-classic/conf/gb2] 

   // DO NOT CHANGE: CGI::Toggle has hard-coded paths
Directory for GBrowse's static images & HTML files? [/usr/local/wormbase/website-classic/html/gbrowse2] 
Directory for GBrowse's temporary data [/usr/local/wormbase/tmp/gbrowse2] 
Directory for GBrowse's example databases [/usr/local/wormbase/website-classic/html/gbrowse2] 
Apache CGI scripts directory? [/usr/local/wormbase/website-classic/cgi-perl/seq]    // Will automatically create a gb2/ subdirectory
Internet port to run demo web site on (for demo)? [8000] 
Apache loadable module directory (for demo)? [/usr/lib/apache2/modules] 
User account under which Apache daemon runs? [www-data] 
Automatically update Apache config files to run GBrowse? [y] n

This will install all the GBrowse libraries into my shared library path. This might not be optimal... 

 $ ./Build test
 $ ./Build install

[tharris@wb-dev: GBrowse-1.988-2nGezp]> ./Build apache_conf
NOTE: Run ./Build reconfig to change existing configuration.

INSTRUCTIONS: Paste the following into your Apache configuration
file. You may wish to save it separately and include it using the
Apache "Include /path/to/file" directive. Then restart Apache and
point your browser to http://your.site/gb2/ to start browsing the
sample genomes.

>>>>>> cut here <<<<<
Alias        "/gb2/i/" "/var/tmp/gbrowse2/images/"
Alias        "/gb2"    "/usr/local/wormbase/website-classic/html/gb2"
ScriptAlias  "/gb2"      "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"

<Directory "/usr/local/wormbase/website-classic/html/gb2">
  Options -Indexes -MultiViews +FollowSymLinks
</Directory>

<Directory "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2">
  SetEnv PERL5LIB "/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5"
  SetEnv GBROWSE_CONF   "/usr/local/wormbase/website-classic/conf/gb2"
</Directory>


<IfModule mod_fastcgi.c>
  Alias /fgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
  <Location /fgb2>
    SetHandler   fastcgi-script
  </Location>
  FastCgiConfig -initial-env PERL5LIB=/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5 -initial-env GBROWSE_CONF=/usr/local/wormbase/website-classic/conf/gb2
</IfModule>

<IfModule mod_perl.c>
   Alias /mgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
   PerlSwitches -I/usr/local/wormbase/extlib/lib -I/usr/local/wormbase/extlib -I/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi -I/usr/local/wormbase/extlib/lib/perl5
   <Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>


GBrowse 1.x stable 

 $ cd /usr/local/wormbase/build
 $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
 $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r stable Generic-Genome-Browser
 $ ln -s Generic-Genome-Browser-stable-anonymous
 $ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib
   Apache root directory (enter  for none)? 
   Apache conf directory? [/etc/apache2] /usr/local/wormbase/website-classic/conf
   Apache htdocs directory? [/var/www] /usr/local/wormbase/website-classic/html
   Apache cgibin directory? [/usr/lib/cgi-bin] /usr/local/wormbase/website-classic/cgi-perl/seq
   GBrowse root for static files? [gbrowse] gbrowse

AceDB

I always build acedb from source. 

$ tar xzf ACEDB-source*    // CAUTION: Tarbomb.
// Requires installation of a whole bunch of things first: libgtk2.0-0 libgtk2.0-dev libglib, byacc, etc, etc
// Modify the makefile: create a target for server programs (xace tace saceserver sgifacerver)
// This is all I care about:
   SERVERS = xace tace saceserver sgifaceserver saceclient
   servers: $(SERVERS)
$ export ACEDB_MACHINE=LINUX_4
$ make servers
$ cd ~acedb
$ ln -s bin-VERSION bin 
$ cp tace xace sgifaceserver saceserver saceclient ~acedb/bin/.
$ sudo chown root:root ~acedb/bin/*

Testing the Installation

At this point, you can test whether the socket server runs correctly. Provided that you have added yourself to the acedb group, you can run the following command: 

 % ~acedb/bin/sgifaceserver ~acedb/wormbase
 // Database directory: /usr/local/wormbase/acedb/wormbase
 // Shared files: /usr/local/acedb
 // #### Server started at 2001-07-23_16:42:31
 // #### host=mondseer.cshl.org  listening port=23100
 // #### Database dir=/usr/local/acedb/elegans
 // ####  Working dir=/usr/local/acedb/elegans
 // #### clientTimeout=600 serverTimeout=600 maxKbytes=0 autoSaveInterval=600

 // Server listening socket 28 created

The line "listening port=23100" indicates that the server is listening to port 23100. Open a new terminal window and use saceclient to confirm that you can communicate with the server: 

% ~acedb/bin/saceclient localhost -port 23100
Please enter userid: anonymous
Please enter passwd:
acedb@localhost> find Sequence
// Response: 65 bytes.

// Found 236493 objects in this class
// 236493 Active Objects
acedb@localhost> quit
// Closing connection to server.
// Client sent termination signal by server.
// Response: 13 bytes.
// A bientot
// Please report problems to acedb@sanger.ac.uk
// Bye

Configuring Acedb to start automatically under xinetd

Install xinetd (not standard in Debian) if you didn't already: 

  $ sudo apt-get install xinetd

Create a configuration file for acedb: 

 $ sudo emacs /etc/xinetd.d/acedb-wormbase 

 # file: /etc/xinetd.d/acedb-wormbase
 # default: on
 # description: wormbase acedb database
 service acedb
 {
        protocol                = tcp
        socket_type             = stream
        port                    = 2005
        flags                   = REUSE
        wait                    = yes
        user                    = acedb
        group                   = acedb
        log_on_success          += USERID DURATION
        log_on_failure          += USERID HOST
        server                  = /usr/local/wormbase/acedb/bin/sgifaceserver
        server_args             = /usr/local/wormbase/acedb/wormbase 1200:1200:0
 }

Edit /etc/services. Although xinetd is not supposed to use /etc/services, the following line must be added: 

acedb-wormbase           2005/tcp

Restart xinetd with the following command: 

# /etc/init.d/xinetd reload (or restart)

You should now be able to talk to the database using saceclient: 

% ~acedb/bin/saceclient localhost -port 2005

MySQL

Installation

Install mysql and various libraries via apt-get if you haven't already: 

 $ sudo apt-get install mysql-server-5.0 mysql-server libdbd-mysql libdbd-mysql-perl

If it fails, then disable innodb by default. edit /etc/mysql/my.cnf file (uncomment the line): 

 #skip-innodb
 $ sudo apt-get purge   mysql-server-5.0 mysql-server  
 $ sudo apt-get install mysql-server-5.0 mysql-server

With this installation, databases are located at /var/lib/mysql. We want to able to write to this directory from the command line, so: 

 $ sudo chmod 2775 /var/lib/mysql

Mysqld will automatically be setup to launch at server boot (rc3 and rc5) -- no need to mess with init scripts.

Set up mysql permissions

# mysql -u root -pPASSWORD
 mysql> grant select on elegans.* to nobody@localhost;

Repeat for:

  • c_briggsae
  • c_japonica
  • c_remanei
  • c_brenneri
  • p_pacificus
  • b_malayi
  • c_elegans_gmap
  • c_elegans_pmap
  • autocomplete
  • h_bacteriophora

Apache2 and mod_perl

Installation

sudo apt-get install apache2
sudo apt-get install libapache2-mod-perl2

Configuration

We will set up WormBase to be a virtual host running on the default port 80. Add the following configuration directives to /etc/apache2/sites-enabled/000-default: 

<VirtualHost *:80>
   Include /usr/local/wormbase/website-classic/conf/httpd.conf
   // ServerName dev.wormbase.org
   // UseCanonicalName on
</VirtualHost>

Be certain to remove or comment out the default configuration.

Modify /usr/local/wormbase/website-classic/conf/httpd.conf to match the new directory layout.

TODO: I NEED TO ACCOUNT FOR OTHER VIRUTAL SERVERS RUNNING ON THE DEVELOPMENT SITE

Important Fix for mod_perl2/mod_dir incompatibility (the index.html problem)

mod_perl2 intercepts Apache requests before any other modules. This means that for locations/directories configured with PerlHandlers that requests for dir or dir/ will NOT automatically redirect to the value of DirectoryIndex. To fix this problem, the lib/Apache/AddWormBaseBanner.pm needs to be modified:

Insert the following: 

# We need two additional modules:
use Apache2::Const -compile => qw(DIR_MAGIC_TYPE OK DECLINED);
use Apache2::SubRequest;

sub handler {
   my $r = shift;
 # --> Copy and paste starting here...
 # A directory request has content-type = httpd/unix directory                                                             
 # we check that the uri ends in a slash, since only in that case                                            
 # do we want to redirect, and finally to avoid redirect loops                                                                                      
 # we only do this on the initial request.                                                                                                
 # You must load Apache2::SubRequest in order to run internal_redirect                                                                                                        
 if ($r->content_type eq 'httpd/unix-directory'
     && $r->uri =~ '/$' && $r->is_initial_req ) {
     #        print STDERR "Accepting Directory Request\n";                                                                                                          
      # warn "internal request";                                                                                                                                                                                
       $r->internal_redirect($r->uri . 'index.html');
       return OK;
   }

Build ePCR NOT DONE

  • e-PCR (modified version, required for e-PCR search page)

This is located in the directory /usr/local/wormbase/e-PCR, which will come into existence after the WormBase site update program wb_update_wormbase.pl has been successfully run (see below for details). Once the directory has been generated, run: 

   $ cd /usr/local/wormbase/e-PCR
   # Edit 'makefile' to run install rather than ginstall, which doesn't exist on Fedora Linux
   $ make
   $ make install   # or just run 'install e-PCR /usr/local/bin'

The file /usr/local/wormbase/e-PCR/README-Wormbase describes the changes that were made to the original e-PCR distribution.

Installing BLAT

Jim Kent's BLAT (blast-like alignment tool) is a fast nucleotide aligner used by the blast search page. If you do not plan to support blast searches, you may safely skip this step. 

# mkdir -p /usr/local/blat/bin ; cd /usr/local/blat/bin
 % wget http://www.soe.ucsc.edu/~kent/exe/linux/blatSuite.33.zip  (for Intel Linux)
% unzip blatSuite.33.zip
% rm blatSuite.33.zip version.doc 11.ooc

Note that this choice gives precompiled binaries for an Intel-based Linux distribution as of March 2006. It would probably be worth checking http://www.soe.ucsc.edu/~kent/exe/linux to see if there is a more up-to-date version than 33. Also, other operating systems will need other binaries. E.g., for Mac OS X, instead run: 

 % wget http://www.soe.ucsc.edu/~kent/exe/osX/blatSuite.33.zip

For other types of operating systems (e.g., Linux on Opteron-based machines), see http://www.soe.ucsc.edu/~kent/exe/ for the available choices.

The blat server will be started automatically by the update script. For reference, the blat server is launched using the following command. 

% /usr/local/blat/bin/gfServer start localhost 2003 \
     /usr/local/wormbase/blat/*.nib & > /dev/null 2>&1

Installing BLAST

The Blast page requires WU-BLAST. This is a closed-source derivative of NCBI's BLAST. However, WU-BLAST is free to academic users (with licensing) and is thought to have performance advantages over NCBI-BLAST; it can be downloaded from http://blast.wustl.edu/. A typical choice of WU-BLAST for Linux is blast2.linux26-i686.tar.gz.

Conversely, the Blast page can be deactivated if you don't want to provide BLAST searches at your site.

By default, WormBase expects WU-BLAST to be installed in /usr/local/wublast. This is the directory structure used by WormBase: 

% ls -l /usr/local/wublast
ls -l /usr/local/wublast
total 72
lrwxrwxrwx  1 root  root     18 May  7 12:26  BLOSUM62 -> matrix/aa/BLOSUM62
-rw-r--r--  1 root  root  46789 Feb  5  1998  HISTORY
-rw-r--r--  1 root  root   6648 Mar  4  1997  README
drwxr-xr-x  2 root  root   4096 May  7  12:46 bin/
lrwxrwxrwx  1 root  root     25 Jul 24  08:20 databases -> /usr/local/wormbase/blast/
drwxr-xr-x  2 root  root   4096 Jan 27  2000  filter/
drwxr-xr-x  4 root  root   4096 Oct  4  1998  matrix/

which can be set up in this manner (adapt to your system): 

$ cd /usr/local/wublast
$ zcat /usr/local/TGZ/blast2.linux26-i686.tar.gz | tar xf -
$ chown -R root:root *
$ mkdir bin
$ mv *fasta tblast* blast* *db xd* memfile pam wu-blastall bin
$ ln -s /usr/local/wormbase/blast databases

The important thing to note is that the databases directory is a symbolic link to /usr/local/wormbase/blast. This is where the update_wormbase.pl script (described in the next section) dumps its BLAST databases.

The WormBase Software

Check out the WormBase software from CVS: 

 $ cd /usr/local/wormbase
 $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository co wormbase-website
 $ mv wormbase-website website-classic

Configure localsdef.pm

  • $HOST

This is the name of the host where the socket server runs. It is set to "localhost" by default.

  • $PORT

This is the port on which the socket server runs, 2005 by default.

  • $ACEPASS, $USERNAME, $PASSWORD

These three items define the acedb username and password.

  • $MYSQL_HOST, $MYSQL_USER, $MYSQL_PASS

These three items define the mysql host, username, and password.

  • $MASTER

This is used only for the WormBase master site. Should be set to 0.

  • $MIRROR

Whether or not the site is a mirror. Should be set to the name of the mirror.

  • $DEVELOPMENT

Whether or not the site is a development site. Internally, this controls the nature of caching on the site. Should be set to 0.

  • $BLAST2WORMBASE, $WORMBASE2BLAST

These two options control where the blast script directs queries, and where those queries are returned. This is provided in the event that a second standalone blast server is provided. If not, these two options should point to: 

$WORMBASE2BLAST=http://your.hostname.org/





Configuring Servers To Start Automatically

The final step is to arrange for Acedb to start automatically and for MySQL to restart if necessary.

Installing MySQL and BLAT monitoring scripts

Run: 

   $ cp -i /usr/local/wormbase/util/admin/blat_server.initd /etc/rc.d/init.d/blat_server

Then run: 

   $ crontab -u root -e

to add the following entries to root's crontab: 

   0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
   0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl

Acedb log rotation

Acedb generates massive log files. To keep these from growing too large, add the following entry to root's crontab (or that of another privileged user): 

   10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl


Installing scripts to verify that the servers are running

Two scripts in the WormBase directory can be used to ensure that the mysql and blat servers are running. To install, them: 

% sudo cp /usr/localwormbase/util/admin/blat_server.initd \
          /etc/rc.d/init.d/blat_server

Place the restart scripts under cron control of a privileged user. These commands will check every hour to see that the servers are running. 

 % sudo crontab -u root -e

0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl

At the same time, you might also wish to automate the rotatation of logs to prevent them from growing to an unwieldy size. You'll find an appropriate log rotation configuration stanza in util/rotate_wormbase_logs and a log rotate script in /usr/local/wormbase/bin/rotatelogs.pl. You will need both. 

# Rotate httpd logs
 10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
 # Rotate acedb logs
 10 1 * * * logrotate /usr/local/wormbase/util/rotate_wormbase_logs

This stanza will check that the acedb server logs do not grow larger than 100 MB.



Testing The Site

At this point, all components of a WormBase installation have been installed. You can test your installation by restarting the various server components of WormBase.

Restarting AceDB

# Via xinetd:
 $ /etc/init.d/xinetd reload (or restart)
 

# ...or using saceclient
 % saceclient localhost -port 2005
 acedb> password:
 acedb> shutdown now

Restarting MySQL

# Via mysqladmin...
 % mysqladmin -uroot -pPASSWORD shutdown
 
 # or using init.d
 $ /etc/init.d/mysql restart

Restarting Apache

When the configuration files have been checked and adjusted, restart Apache with the following command: 

 $ /etc/init.d/apache restart

Check /usr/local/wormbase/logs/classic-error_log for WormBase-specific errors and /var/log/apache2/error_log for general errors.

BLAT

% /usr/local/blat/bin/gfServer start localhost 2003 \
     /usr/local/wormbase/blat/*.nib & > /dev/null 2>&1

Blocking robots

It can be useful to block search engines (such as Google) from crawling over one's mirror. To do this, go to /usr/local/wormbase/html, and make a file called "robots.txt" with the following contents: 

   User-agent: *
   Disallow: /

Updating Production Nodes to match this reality

1. Create /usr/local/wormbase/website-classic

2. Move all website files into website-classic

3. Move database to /usr/local/wormbase

4. Create /usr/local/wormbase/logs

5. Install Perl Modules as described above

6. Install GBrowse as described above

7. Update admin module for pushing software to production (and for maintaining staging module)

AUTHOR

Todd Harris

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