Installing a local LAPPS/Galaxy instance

This page describes setting up a local LAPPS Grid Galaxy instance for quick experimentation. There is considerable overlap with the page on installing a production instance and it would be a good idea to skim through that page as well, but this page should be mostly stand on its own. The main difference with installing a production in stance is that no PostgreSQL installation is needed here.

For a list of known issues and workarounds see galaxy-known-issues.html.

Prerequisites

The following are required:

Install scripts for some of the above are available at http://downloads.lappsgrid.org/scripts, these scripts are only tested for Ubuntu though. The only esoteric prerequisite is LSD (LAPPS Services DSL, a Groovy based Domain Specific Language for scripting services on the LAPPS Grid). You can access the LSD repository. and click the “latest binaries” link to get a zip archive with a jar file and a file named lsd which you should make available as a command by putting it on your shell path. You could also peek at the Ubuntu install script for hints.

Installing the instance

First you get the code in the Galaxy and GalaxyMods repositories:

$> cd /home/galaxy
$> git clone http://github.com/lappsgrid-incubator/Galaxy.git galaxy
$> git clone http://github.com/lappsgrid-incubator/GalaxyMods.git mods

It does not matter where on the local file system you do this, but you need to save these in directories named galaxy and mods (later steps depend on those exact names) and the two repositories need to be in the same directory. For this example we use /home/galaxy.

You need to determine what branches to use for both repositories. Unfortunately, there is not a lot of help on this in those repositories and there is no published list of dependencies. The page for installing a production instance says to use the lapps branch of the Galaxy repository and the master branch of the GalaxyMods repository.

Next you need to run the patch-galaxy-ini.sh patch script from the directory where galaxy and mods are located:

$> cd /home/galaxy
$> chmod +x patch-galaxy-ini.sh
$> ./patch-galaxy-ini.sh /home/galaxy

This script takes mods/config/galaxy.ini, makes some changes to it and saves the result in galaxy/config/galaxy.ini. Part of what this script does is technically not necessarily needed for a local install (for example, it gets a password for the PostgreSQL database) but that is okay.

For the simplest install we use SQLite instead of PostgreSQL. Unfortunately, the mods/config/galaxy.ini configuration file in mods/config/galaxy.ini assumes PostgreSQL so we need to change a few lines in mods/config/galaxy.ini:

#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
database_connection = postgresql://galaxy:SA4.rY5l0kP!EYkjM%2l8.s!@localhost/galaxy
==>
database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
#database_connection = postgresql://galaxy:SA4.rY5l0kP!EYkjM%2l8.s!@localhost/galaxy

database_engine_option_server_side_cursors = True
==>
#database_engine_option_server_side_cursors = True

Finally, you start galaxy from the root galaxy directory:

$> cd /home/galaxy/galaxy
$> ./run.sh

First time you run this a lot of Python modules will be downloaded and the whole process takes a while. Also the first time the SQLite database will be set up and modified many times. After the first time start up should be much faster. After executing the runs.sh script a LAPPS/Galaxy instance should be running at http://127.0.0.1:8000.