SIFTER Installation

The installation instructions are written for each of the administrators, as well as the individual analyst (end user). All of the SIFTER code is written as Perl programs and modules or Java applets and classes.

SIFTER is complex, requiring many cooperating pieces of software. It's installation is similarly complex. Groups with relatively small amounts of data or who do not have people with the skills to perform the various administrator roles may wish to ask some other group which has the administrator resources to host their data and assist in loading the data.

Installations come in two flavors, if you will. The first and most complex occurs when you first attempt to install and use SIFTER. This entails verifying all software, initializing a database and loading data, creating all realm files and installing software for the web server and clients. The second form is a simple update of the software which only requires refreshing the server and client software.

Your First and Most Complex Install

The order of installation is important. You need to do a complete installation in this order:

1. Extract the SIFTER Source Files

SIFTER is distributed as a compressed tar file. You should first extract the tar file in some directory (perhaps $HOME/src). We will refer to this directory as the SIFTER distribution directory. Extract the files in the normal way:

    tar xzf sifter*.tgz
       or
    gzip -c sifter*.tgz | tar xf -

2. Install Required Perl Modules

SIFTER makes extensive use of Perl and the various modules that are available on the Net. You must be using a Unix version of Perl at version 5.6 or higher, although Perl 6.0 is not supported. A few modules beyond the normal set of modules the standard Perl installation are required. You will find the complete list in the file PERL.MODULELIST found in the distribution. Install these modules before continuing.

3. Create a Database for the Demo

If you are going to install the demo system, you'll need to create a database for it. While you COULD create one database, install the demo and then reuse the database for your project, we recommend you create a separate database for the demo and another later on for your project. It's useful to keep the demo around for testing and to try out administrative changes.

The database for the demo can be quite small - requiring only 2MB of data in even the most complex databases. The actual data to be loaded is less than 1 MB total.

4. Install and Try the Demo

If this is your first experience with SIFTER, you really should install the demo. It will completely check out your installation and make sure you understand the names and database and web questions. There are plenty of ways an installation might fail. Installing the demo will carefully check all the known possibilities and tell you exactly what is missing. Get all the details here.

5. Decide on a Project Name

Now you need to decide what SIFTER projects do you wish to define. A SIFTER project is simply a collection of analyses you wish to look at together and will always correspond to your existing analysis projects. The only issue here is to determine which analyses should be grouped together in one database. For example, you might have have people working on PROGERIA and GLAUCOMA. In this case you will almost always want to define two SIFTER projects, one for PROGERIA and another for GLAUCOMA.

Defining a separate SIFTER project for each group of analyses will keep the results separate and prevent analysts from one project from seeing results in another project. The amount of data is seldom a criteria to combine or separate projects.

6. Create a Database for your Project

Now it's time to create a real database for your project. Hopefully your DBA has gained a little insight from the demo. Your DBA will be asking how many maps and results you have and how big they are. What guidelines we can provide are documented here.

6. Create the Project

If you installed the demo, this will be very easy. A script will prompt you for very similar information as with the demo. Once you understand what will be asked for, this will only take a couple of minutes. Get all the details here.

7. Install the SIFTER Client Software

The client software is only about loading your maps and results into the SIFTER database for a project. It may well be this is only done by one person in your project. In another project, each analyst might load data into SIFTER. This step is about installing the Perl scripts which will load the maps and results. Get all the details here.

8. Administer SIFTER Attributes

SIFTER is a data driven system. This allows us to minimize dependencies SIFTER has on your data. This makes SIFTER more flexible at some cost of complexity. Before loading maps and results into SIFTER, you must define to SIFTER a set of attributes of the data. SIFTER already comes with many preset attributes which may well be enough for smaller projects. Larger, more complex projects will want to augment the defaults. Get all the details here.

9. Load Your Data into SIFTER

This is the last step before SIFTER is usable - getting your maps and results into the SIFTER database. Client scripts were installed earlier so everything is now ready. You should load your maps before loading results, as one of the attributes for a result is the map name. Then load your results. Perl and shell scripts can help automate this process. Get all the details here.

Last. Using SIFTER

The point of this entire process has been to get your maps and results into SIFTER so the analysts can search through them and find 'interesting results'. This end user interface is provided entirely via a web interface. Details are available here.

Simple Install - Refreshing Your Software

At some point after you have SIFTER installed and running, you'll want to update your software. Fortunately, this is much easier the second and subsequent times around as your can be pretty sure your Perl modules and database are correct.

Nonetheless, this is new software, so you'd be wise to install the demo again, just to be sure nothing dramatic changed. Once you are confident the new software should work, do not re-create your project (step (6) above), but rather just update your server.

1. Extract the SIFTER Source Files

This is exactly the same as step (1) above.

2. Re-Install the SIFTER Server Software

If you installed the demo, this will be very easy. A script will prompt you for very similar information as with the demo. Once you understand what will be asked for, this will only take a couple of minutes. Get all the details here.

3. Install the SIFTER Client Software

This is exactly the same as step (7) above.

4. Using SIFTER

This is exactly the same as step (Last) above.

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