Administration:Installing WormBase
Contents
- 1 Address
- 2 Hardware
- 3 Server Configuration
- 4 Perl modules
- 5 Generic Genome Browser
- 6 3rd-party Support Applications
- 7 The WormBase Software
- 8 Cronjobs
- 9 Testing The Site
- 10 Updating Production Nodes to match this reality
- 11 AUTHOR
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
Basic Directory Layout
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!
Apache2: /usr/local/apache2 MySQL data directory: /usr/local/mysql/data
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
- 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
- External Perl libraries: /usr/local/wormbase/website-classic/extlib, owner=tharris group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/website-classic/extlib $ chgrp wormbase /usr/local/wormbase/website-classic/extlib $ chmod 2775 /usr/local/wormbase/website-classic/extlib
- /usr/local/wormbase/logs, owner=root group=wormbase mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/logs $ chgrp wormbase /usr/local/wormbase/logs $ chmod 2775 /usr/local/wormbase/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
See Managing Perl Libraries for details on how to build and install required Perl modules.
Generic Genome Browser
See Managing GBrowse for details on how to build and install GBrowse.
3rd-party Support Applications
Apache2 and mod_perl
I prefer to build httpd and mod_perl from source; it seems easier than waiting for package repositories to be updated.
Installation
Assuming you have already fetched the source into ~/src:
# Build httpd 2.2.11 cd ~/src tar xzf httpd-2.2.11.tar.gz cd httpd-2.2.11 ./configure --enable-mods-shared=all // We can enable modules in httpd.conf later make sudo make install
# Build mod_perl2-0.4 cd ~/src cd mod_perl-2.0.4 // Get rid of some (possible) cruft sudo rm -rf /usr/local/wormbase/extlib/lib/perl5/i686-linux-thread-multi/Apache2 \ /usr/local/wormbase/extlib/lib/perl5/i686-linux-thread-multi/ModPerl \ /usr/local/wormbase/extlib/lib/perl5/i686-linux-thread-multi/mod_perl2.pm make clean perl -I/usr/local/wormbase/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib // When prompted for the apxs path, enter: /usr/local/apache2/bin/apxs make sudo make install
Configuration
- Set httpd to listen on port 8080.
$ sudo perl -p -i -e's|Listen 80|Listen 8080|' /usr/local/apache2/conf/httpd.conf
- Set up a virtual host for WormBase on port 8080
$ sudo emacs /usr/local/apache2/conf/extra/httpd-vhosts.conf <VirtualHost *:8080> Include /usr/local/wormbase/website-classic/conf/httpd.conf PerlOptions +Parent PerlSwitches -Mlib=/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi \ -Mlib=/usr/local/wormbase/extlib/gbrowse1/i686-linux-thread-multi \ -Mlib=/usr/local/wormbase/extlib/gbrowse1 \ -Mlib=/usr/local/wormbase/extlib/lib/perl5/i686-linux-thread-multi
# PerlInterpStart 2 # PerlInterpMax 2 <Directory "/usr/local/wormbase/website-classic/html"> DirectoryIndex index.html # Order deny,allow # Deny from all </Directory> </VirtualHost>
- Enable virtual hosts in httpd.conf
$ sudo perl -p -i -e's|\#Include conf/extra/httpd-hosts.conf|Include conf/extra/httpd_hosts.conf|' \ /usr/local/apache2/conf/httpd.conf
Set up httpd to run under inet.d
Save the following file to /etc/init.d/httpd:
#!/bin/bash # # Startup script for the Apache Web Server # # chkconfig: - 85 15 # description: Apache is a World Wide Web server. It is used to serve \ # HTML files and CGI. # processname: httpd # pidfile: /usr/local/apache2/logs/httpd.pid # config: /usr/local/apache2/conf/httpd.conf # Source function library. . /etc/rc.d/init.d/functions if [ -f /etc/sysconfig/httpd ]; then . /etc/sysconfig/httpd fi # This will prevent initlog from swallowing up a pass-phrase prompt if # mod_ssl needs a pass-phrase from the user. INITLOG_ARGS="" # Path to the apachectl script, server binary, and short-form for messages. apachectl=/usr/local/apache2/bin/apachectl httpd=/usr/local/apache2/bin/httpd pid=/usr/local/apache2/logs/httpd.pid prog=httpd RETVAL=0 # The semantics of these two functions differ from the way apachectl does # things -- attempting to start while running is a failure, and shutdown # when not running is also a failure. So we just do it the way init scripts # are expected to behave here. start() { echo -n $"Starting $prog: " daemon $httpd $OPTIONS RETVAL=$? echo [ $RETVAL = 0 ] && touch /var/lock/subsys/httpd return $RETVAL } stop() { echo -n $"Stopping $prog: " killproc $httpd RETVAL=$? echo [ $RETVAL = 0 ] && rm -f /var/lock/subsys/httpd $pid } reload() { echo -n $"Reloading $prog: " killproc $httpd -HUP RETVAL=$? echo } # See how we were called. case "$1" in start) start ;; stop) stop ;; status) status $httpd RETVAL=$? ;; restart) stop start ;; condrestart) if [ -f $pid ] ; then stop start fi ;; reload) reload ;; graceful|help|configtest|fullstatus) $apachectl $@ RETVAL=$? ;; *) echo $"Usage: $prog {start|stop|restart|condrestart|reload|status" echo $"|fullstatus|graceful|help|configtest}" exit 1 esac exit $RETVAL
Set which runlevels httpd will run under:
chkconfig --add httpd chkconfig --level 2345 httpd on chkconfig --list
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; }
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 ACeDB 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:
$ sudo /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).
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
e-PCR
- 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.
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
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/
Cronjobs
Set up the following cronjobs:
Log Rotation (root cron)
# Rotate WormBase logs 10 1 * * * /home/todd/projects/wormbase/admin/maintenance/rotate_httpd_logs.pl
For nodes running acedb, add the following entry which deals with its massive log files:
# Purge epic ACEDB logs 35 * * * * /home/todd/projects/wormbase/admin/maintenance/purge_acedb_logs.sh
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
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 (toddwharris@gmail.com)