Localinstall

mojones edited this page Nov 12, 2012 · 1 revision

Installing afterparty on a local machine

This guide will outline the steps required to install afterparty on a local machine. The instructions were written assuming a clean installation of Ubuntu server 12.04, but should be similar for other recent distributions of linux. If you have no pressing need to install afterParty on a physical (rather than virtual) machine, then we suggest that you take a look at the virtual machine instructions as they are much simpler.

Java

Download and install Sun Java 1.6. Afterparty and Interproscan do not work well with the openJDK After installing Java, set the JAVA_HOME environment variable and add the /bin directory to your PATH.

Git

Install git. The latest version is fine. apt-get install git will probably do the job on Debian-based systems like ubuntu.

Grails

Install Grails 2.0.3. Afterparty will probably work with more recent versions, but you will have to upgrade the repository manually which will cause it to be out of sync with the development branch.

Set up afterparty

Use git to clone the Afterparty repository:

git clone git://github.com/mojones/AfterParty2.git

From the main afterparty directory, run grails upgrade. Copy the file afterparty.config.groovy.sample to your home directory and rename it to afterparty.config.groovy. .

Postgresql

Install Postgresql 9 (sudo apt-get install postgresql-9.1). Create a new user with the ability to create databases. Edit your pg_hba.conf file to allow local and host md5 authentication. Create a new database, owned by your afterparty user, to hold afterparty data and run the afterparty.sql script to create the schema. Edit the afterparty.config.groovy file with the username and password of your database superuser and the name of the database that you have created.

BLAST

Install NCBI BLAST

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

and set the executable paths in your afterparty.config.groovy. Download the uniprot database dump:

ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/

and format it to create a BLAST database. Put the path to the BLAST database in your afterparty.config.groovy.

If you'd like to carry out BLAST annotation using a different database, just replace uniprot above with the FASTA file of your choice.

MIRA

Download and extract MIRA:

http://www.chevreux.org/projects_mira.html

and set the path to the executable in afterparty.config.groovy.

InterProScan

Download and install InterProScan 5 using instructions from here:

http://code.google.com/p/interproscan/wiki/RunningStandaloneInterProScan5

And set the path in afterparty.config.groovy.

Running afterparty

Navigate to the root directory of afterparty and run grails run-app. The first time this is run on a new system it will probably take a while to download all the plugin dependencies. By default, grails will run on port 8080.

Questions / comments / bugs

Contact martin.jones@ed.ac.uk