Let's assume that you have already downloaded and unpacked the goalie.zip file in some directory. Let's also assume you called this directory goalie.
You should see the following directory structure
| goalie\README | A simple notice. |
| goalie\INSTALLATION | A file containing installation instructions. |
| goalie\goalie.exe | The executable. |
| goalie\data\ | A directory containing example data (Yeast Cell Cycle data from Stanford). |
| goalie\.goalie-init | An example init file. |
Other files and directories may appear, but they are not relevant to these instructions.
GOALIE depends on the GO database, which is accessed through an ODBC driver.
You should get and install the GO database by downloading it from http://www.godatabase.org/dev/database/. Follow the instructions you find on the GO site. Installing on the Mac is usually straightforward. Installing on Windows may be slightly easier if you use Cygwin.
Make sure that you have installed one of the seq or seqlite GO database distributions.
The GO database requires MySQL, which you can download from http://www.mysql.org
GOALIE also requires the MySQL ODBC/Connector, which can be downloaded and installed from the same place. We suggest that you start MySQL as a Windows service; follow the MySQL instructions to do so.
In order to make you GO databases visible by GOALIE, you must register them with the Windows ODBC manager. To do so you need to start the Data Sources (ODBC) shortcut from the Administrative Tools folder in the Windows Control Panel. Follow the instructions there, and add a "data source" for the databases. Remember the names you give the data sources, the user-name you used, and the passwords, as you will need them in the next step. The Data Sources (ODBC) tool allows you to test the connection, so we assume you have up and running connections at this point.
First of all copy your .goalie-init file to your "home" directory. In Windows XP this should be
C:\Documents and Settings\your-user-name.
Then edit it with any editor (as long as it is Emacs, to paraphrase Mr. Ford on the colors available for the Model T :) ). At this time you will notice that the .goalie-init file is a Common Lisp file. You may not be familiar with Common Lisp having spent your time with Perl, Python, C/C++, Java and whatnot so far :), but the bottom line is that everything after a semicolon ; up to the newline is a comment.
Common Lisp has an extremely simple syntax:
'(' <operator> <arg1> <arg2> ... <argN> ')'
You will see several setf commands in the file. They are simple assignments of values to variables. The general form is
(setf <some-name> <some-value>)
As an example, consider the command
(setf *go-db-name* "<GO ODBC DATASOURCE NAME HERE>")
This sets the name *go-db-name* to the string, as usual bounded by double quotes ("), at the right. In this case you will need to replace the string
"<GO ODBC DATASOURCE NAME HERE>"
with the name of the GO ODBC data source you used while setting up the connection to the ODBC driver; e.g you may end up with
(setf *go-db-name* "GO_DB")
Just change all the strings to suit your configuration and you should be in business.
Double click on goalie.exe or type in goalie.exe at the command line.
You should see the main window up and running. Just check the GO Databases->Ensure Connections menu and look what values are contained in the panel that is popped up. They should reflect your settings from the init file.
Should they not, you can change them. You can also run the Windows Data Sources (ODBC) tool from the panel.
Try to load a GO associations file, from the File->Open menu. If something is amiss, you will get an error message at this point.
We know the setup is currently very laborious and complicated and we are working to fix this. Meanwhile send email to marcoxa [@t] cs.nyu.edu to report problems and make suggestions (please DO so, if we don't get reports, we can neither fix problems nor make improvements).
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