Galaxy Installation

The installation procedure is simple and is nearly identical for UNIX, Windows and Mac computers. Requirements:

To find out what version of python you must type: 

python -V

at a command line. All other modules, the server, the database and the templating engine are packaged with galaxy. You can obtain the most up to date source code via anonymous svn at http://coltrane:8192/svn/universe/prototype/branches/james-wsgi Example: 

svn co http://coltrane.bx.psu.edu:8192/svn/universe/prototype/branches/james-wsgi galaxy_dist

The code you check out this way is typically identical to the code run at the Galaxy Test server: http://test.g2.bx.psu.edu. Once you have the distribution you can periodically update it with the: 

svn update

command, executed in the repository that you have checked out.

Once you have the source code switch to the galaxy_dist directory and make copies of the following files: universe.conf.sample, tool_conf.xml.sample and test.conf.sample. Typically we name the copies as universe.conf, tool_conf.xml and test.conf. If you name them like that the system can make use of them without any further configuration.

At this point galaxy is ready to run via the following command: 

python universe.py

This will start up the server on localhost and port 8080 so check http://localhost:8080 to see whether it is working.

Testing the distribution

The tests directory contains a number of programs that will verify that the distribution works correctly. To run these programs invoke them from the command line like so: 

python base_test.py

these will connect to the localhost:8080 as user testuser. You can connect to other urls say http://myserver.com:8090 by passing it via command line: 

python base_test.py  http://myserver.com:8090 testuser

Note that some tests pass only if you have the required tools available.

Self test

In your root directory the file test.conf can be used to self test your galaxy distribution. Once galaxy is running go to the http://your-galaxy/test url. The tests listed in test.conf will be run and displayed in the browser. If you open a new tab (or window) you can follow on your site what the tests are actually doing.

Customize the configuration

The server can be passed various configuration options. Use: 

python universe.py -h

to see all the flags that you can set during runtime. All configuration files are in text format and can be edited. Most options should be self-documenting. View the run.sh shell script for further configuration tips.

Tip: To optimize startup time create a smaller tool configuration file that contains only the tools you need then pass this file with the -x flag. 

python universe.py -x small.xml

Svn tips for developers

These are tips for developers that have access to the development machines. The code below checks out the trunk, a new directory called trunk: 

svn co svn+ssh://coltrane.bx.psu.edu/depot/projects/universe/svnroot/prototype/branches/james-wsgi galaxy_2.2

To switch to branch 2.1 do the following in the root of your distribution: 

svn switch svn+ssh://coltrane.bx.psu.edu/depot/projects/universe/svnroot/prototype/branches/universe-2.1

Galaxy version and svn

Galaxy version and svn?