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INSTALL.md

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============= Quick Install

Before starting you'll need apache and mod_perl installed. You are also advised to read the full installation instructions available on http://www.biomart.org/

Please note that the example supplied, conf/registryURLPointer.xml, contains details of Ensembl Genomes release 22 mart databases from the Ensembl Genomes public MySQL server mysql.ebi.ac.uk.

This should only be used for testing, and should NOT be used for running your own mart server. For running production marts, please download the MySQL dumps from ftp://ftp.ensemblgenomes.org/pub/current and load onto your own local MySQL server.

Setup

Create a file conf/settings.conf (based on settings.conf.example).

Change the following line to a location where temporary files can be written by the web user:

resultsDir1=/path/to/test/files

Change the followings line in conf/settings.conf:

apacheBinary=/path/to/apache/bin/httpd
serverHost=localhost
port=5555

Change the following line in conf/log4perl.conf to specify the log location:

log4perl.appender.logFile.filename = /path/to/logs/log4perl_log
  1. Using helper scripts =======================

Alternatively, use the standalone shell scripts provided:

# configure and start Apache (accepts defaults)
cd eg-biomart-perl
export APACHE_HOME=[path to Apache]
./redo.sh conf/registryURLPointer.xml 

# (re)start the apache server
./restart.sh

# stop the apache server
./stop.sh

  1. Direct configuration =======================

    configure biomart

    cd eg-biomart-perl perl bin/configure.pl -r conf/exampleMartURLLocation.xml

Follow the prompts, if you unsure what to answer hit return.

# run your standalone apache instance 
cd eg-biomart-perl
[path to Apache]/bin/httpd -d $PWD

(the path needs to be the same as chosen in step one of your configuration)

Point your browser to http://localhost:5555 (or change the port if you chosen a different option in the configuration step)

If you are having problems or need more information consult the documentation available on www.biomart.org. You can also consult the Ensembl Genomes development team on [email protected] or [email protected].