Please read this before downloading Sockeye 0.8.3

Installing and uninstalling

1. Sockeye installs using InstallAnywhere from Zero G. At the download page, you will be offered a signed applet from Zero G. If you accept it, you should be able to do either an automatic or a manual install. If you decline the applet, you will be able to do only a manual install.
2. Instructions for the manual install are given on the the download page, below the download links.
3. Sockeye can easily be uninstalled. On Linux / Windows, run the Uninstall_Sockeye... shell script / application file in the UninstallerData subdirectory under the Sockeye installation directory. On Windows, you can also use Control Panel > Add or Remove Programs.
4. Mac OS X: When Java3D is available for OS X, we will make a version of Sockeye available for this OS. See ADC.

Java

1. Sockeye is a Java application. You can download a version that is bundled with its own Java (JRE)/Java3D, or a smaller file that has no bundled Java. If you choose the installer that has no Java, you must also install appropriate versions of Java and Java3D in order to run Sockeye.
2. The bundled Java is 1.4.1_01; the bundled Java3D is 1.3.1 beta.
3. Platforms
   1. Linux - We have tested on RedHat 7.2 and 8.0. Sockeye runs on SuSE 8.1 Pro, but has been tested less on this OS.
   2. Windows - We have tested on Win2K, and on XP Pro and Home.
4. Installer with bundled Java VM
   1. You do not need to have Java or Java3D installed outside of Sockeye in order to run Sockeye. The installer will install the Java that Sockeye needs.
   2. Linux - Download: ~50 MB. Installed application: 73+ MB.
   3. Windows - Download: 21+ MB. Installed application 50+ MB.
5. Installer without bundled Java VM
   1. To run Sockeye you must also install appropriate versions of Java and Java3D. Current bundled versions are listed above.
   2. Linux - Download: 8 MB. Installed application: 9+ MB.
   3. Windows - Download: 9 MB. Installed application: 10 MB.

Windows, Java3D, DirectX and OpenGL

1. For Windows, we offer installers with either DirectX or OpenGL versions of Java3D. Differences are discussed here.
2. If you have problems with one of the versions, please uninstall it and try the other.
3. The DirectX version requires a recent version of DirectX (see above Java3D link). We have tested v0.8.3 with Microsoft's current version, 9.0a, on Win2K and XP Pro. You can find the version installed on your computer by running Start > Run > dxdiag. If you need to upgrade your DirectX version, you can get the latest version here.

RAM

1. We have run Sockeye on PCs with between 192 MB and 1 GB of RAM.
2. This prerelease allows Sockeye's Java a maximum of 64 MB RAM. We are exploring giving Sockeye more RAM than this, but have temporarily put two limits into Sockeye to prevent OutOfMemory errors on large datasets. Please see Limitations in the online Help.

Graphics card

1. Because Sockeye is a 3D application, it demands far more graphics card power than a 2D genomic browser.
2. The development team works with cards that are at least at the level of a GeForce2 MX. A card of this level still gives sluggish 3D rotations with a display showing, e.g. all genes on human chromosome 1.

Installed directory structure

Sockeye installs the following directory structure. You can choose the install_directory.

• install_directory - default_config.xml and user_config.xml, sockeye.log (runtime error messages), ...
• data/GFF - example GFF files
• help - properties file for online Help frame
• images - GIF and JPG files
• jre - Java JRE with Java3D
• lib - JAR files
• models - VRML models for 3D features
• UninstallerData - uninstaller files

Updates

Updates will be available frequently. Please subscribe to sockeye-announce@bcgsc.ca for release information.

Source code

Source code will be made available at a later date.

Last modified: 2003_05_02, 13h47