Wormmart administration

Overview

WormMart is WormBase's implementation of the BioMart data warehouse.

Official BioMart Documentation

Basic Server Configuration

Create groups

sudo addgroup wormbase
sudo addgroup biomart
# Add yourself to the groups
sudo usermod -a -G biomart, wormbase acabunoc

Create directories

Create a directory for GBrowse. For now, we're maintaining GBrowse on dedicated hardware completely distinct from the rest of the web application. This makes updates significantly easier, although it increases maintenance (ie boilerplate headers and footers are maintained in two places). We'll also keep gbrowse inside a wormbase/ directory should we wish to install other components on these servers at a later date.

$ sudo mkdir -p /usr/local/wormbase
$ sudo chgrp -R wormbase /usr/local/wormbase
$ sudo chmod 2775 /usr/local/wormbase

Install prerequisites (Debian)

// Update apt
$ sudo apt-get update

// Make tools
$ sudo apt-get install gcc make

// expat
$ sudo apt-get install expat libexpat1 libexpat1-dev

// GD support
$ sudo apt-get install libgd2-noxpm libgd2-noxpm-dev

// Graphviz, now apparently required by BioPerl
$ sudo apt-get install graphviz

// Curl
$ sudo apt-get install curl

//CVS
$ sudo apt-get install cvs

//Java
$ sudo apt-get install sun-java5-jre

Install Perl 5.10.1 or greater

You'll need Perl version 5.10.1 or greater.

Debian:

$ sudo apt-get install perl

NOTE: This version of Perl on Debian Lenny doesn't ship with perl.h. You won't be able to build mod_perl without it! You should probably build from source.

Building from source:

bash> cd ~/src
bash> curl -O http://www.cpan.org/src/perl-5.10.1.tar.gz
bash> cd ~/build
bash> tar xzf ../src/perl-5.10.1.tar.gz
bash> cd perl-5.10.1
bash> ./Configure -des
  // Or, to install in a local path:
bash> ./Configure -des -Dprefix=$HOME/website/perl/5.10.1
  // if mod_perl doesn't work properly, I had to install like this:
bash> CFLAGS='-m64 -mtune=nocona' ./Configure -des -A ccflags=-fPIC
bash> make
bash> make test
bash> sudo make install

Install Apache2

If you're running Debian, get rid of the installed apache. The default layout is just plain annoying.

$ sudo apt-get remove apache2

# Build httpd 2.2.15
cd ~/src
curl -O http://apache.raffsoftware.com/httpd/httpd-2.2.15.tar.gz
tar xzf httpd-2.2.15.tar.gz
cd httpd-2.2.15
./configure --enable-mods-shared=all
make
sudo make install

Apache Configuration

Edit the primary httpd.conf file (/usr/local/apache2/conf/httpd.conf) with the appropriate port, virtual host, and fcgi settings:

• Set httpd to listen on your desired port. In the examples below, we assume port 8080.

# Edit "Listen 80" to read
Listen 8080

Install mod_perl

cd ~/src
wget http://perl.apache.org/dist/mod_perl-2.0-current.tar.gz
tar zxvf mod_perl-2.0-current.tar.gz
cd mod_perl-2.0.4 
perl Makefile.PL \
    PREFIX=/usr/local/apache2 \
    MP_APXS=/usr/local/apache2/bin/apxs

Add to httpd.conf:

LoadModule perl_module modules/mod_perl.so

Then,

sudo make
sudo make install

Downloading martj

Download: ftp://anonymous@ftp.ebi.ac.uk/pub/software/biomart/martj_current/martj-bin.tgz

tar -zxvf martj-bin.tgz

Downloading biomart-perl

cd /usr/local/wormbase/biomart/
cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart login

The password you need to enter when prompted is CVSUSER.

cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart \
    co -r release-0_7 biomart-perl

Note: you may not be able to connect to cvs from wb-blast. If so, checkout code somewhere else and move over to /usr/local/womrbase/biomart/biomart-perl

Install Requisite Perl Modules

cd /usr/local/wormbase/biomart/biomart-perl
perl bin/configure.pl -r conf/registryURLPointer.xml

my output:

Spreadsheet::WriteExcel
Template::Constants
Log::Log4perl
Test::Exception
Mail::Mailer
DBI
Template::Plugin::Number::Format
XML::Parser
List::MoreUtils
Exception::Class
CGI::Session::Driver::db_file
LWP::UserAgent
Spreadsheet::WriteExcel::Big
Number::Format
CGI::Session
XML::DOM
Template
OLE::Storage_Lite
Readonly

install the perl modules you are instructed to by this script

cpan -i Module::Name

MySQL

Installation (>= 5.1)

We need a newer version of mysql than is available from the package manager. We'lll install the binary for x86_64.

$ sudo groupadd mysql
$ sudo useradd -g mysql mysql
$ sudo usermod -a -G mysql tharris
$ cd /usr/local
$ sudo gunzip < /path/to/mysql-VERSION-OS.tar.gz | sudo tar xvf -
$ sudo ln -s full-path-to-mysql-VERSION-OS mysql
$ cd mysql
$ sudo chown -R mysql .
$ sudo chgrp -R mysql .
$ sudo scripts/mysql_install_db --user=mysql  // may be necessary to remove /etc/mysql/my.cnf first
$ sudo chown -R root .
$ sudo chown -R mysql data
$ sudo chmod 2775 data // I like to be able to write to my datadir

// Copy the configuration file
$ sudo cp support_files/my-medium.cnf /etc/my.cnf

// It may be necessary to add the following to my.cnf if back end nodes
// don't have fully qualified domain names
skip-name-resolve

// Set up mysql to start up automatically
$ sudo cp support_files/mysql.server /etc/init.d/.
$ cd /etc/rc3.d
$ sudo ln -s ../init.d/mysql.server S90mysql
$ cd ../rc5.d
$ sudo ln -s ../init.d/mysql.server S90mysql

// Start it up and set a root password.
$ sudo /etc/init.d/mysql.server start
$ mysqladmin -u root password 'PASSWORD'

Databases

MySQL databases will be mirrored over directly as part of the production update process. They should be located in /usr/local/mysql/data. Symlinks, using the symbolic name of the database, point to the current version:

 c_elegans -> c_elegans_WS211

Privileges

$ mysql -uroot -p
$ mysql> create use mart_admin
$ mysql> grant select on `wormmart_%`.* to 'mart_admin'@'localhost'

Berkeley DB

Install Berkeley DB

save to /usr/local/src http://www.oracle.com/technology/software/products/berkeley-db/htdocs/popup/db/5.0.21/db-targz.html

cd /usr/local/src/
sudo gunzip < /path/to/berkleydb.tar.gz | sudo tar xvf -
cd build_unix
../dist/configure
make
make install
cd ../..
echo /usr/local/BerkeleyDB.3.2/lib >> /etc/ld.so.conf
ldconfig

Then install the following perl modules:

DB_File
XML::Simple
DBD::mysql  <-- may have to install from source
Apache2::PerlSections

2.4.3 Configuring

2.4.3.1 Configuring the BioMart Perl API

Configuration of the Perl API requires a single step. Change into the biomart-perl directory, then type:

perl bin/configure.pl -r conf/registryURLPointer.xml

where registryURLPointer.xml is the registry file you wish to use from the conf folder. The first question the configure script will ask is:

Do you want to install in API only mode [y/n] [n]:

Type y to install the API only. During configuration it may point out that required Perl modules are missing. If this happens, follow the steps detailed in the prerequisites section above to install these missing Perl modules. When it has completed successfully, you will see this final message:

Looks good.... you are done.

2.4.3.2 Configuring MartView

in conf/settings.conf

[httpdSettings]
apacheBinary=/usr/local/apache2
serverHost=localhost
port=9002
# to use proxying set the proxy port below (even if its 80) and set serverHost as your proxy host
proxy=
# if apxs or apxs2 is not in default directory where httpd lives, you may set this param to point to apxs/2
apxs=
location=biomart

Reinstalling BioMart

So, sometimes wormmart gets a redirect problem that you can fix by reinstalling!

1. reinstall biomart-perl

cd /usr/local/wormbase/biomart/
cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart login

The password you need to enter when prompted is CVSUSER.

cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart \
    co -r release-0_7 biomart-perl

Note: you may not be able to connect to cvs from wb-biomart. If so, checkout code somewhere else and move over to /usr/local/womrbase/biomart/biomart-perl

2. copy over necessary files

• conf/httpd.conf.bak
• conf/templates/default
• conf/settings.conf

3. Change the permissions for conf/templates/cached

$ sudo chmod 777 conf/templates/cached

3. Make sure you kill all previous wormmart processes

4. Run the following from the biomart-perl directory:

$ sudo perl bin/configure.pl -r conf/wormMartRegistry.xml --clean; 
$ cp conf/httpd.conf.bak conf/httpd.conf; 
$ sudo /usr/local/apache2/bin/apachectl -d /path/to/biomart-perl -f conf/httpd.conf