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. Instructions for the manual install are given on the the download page, below the download links. If you decline the applet, you will be able to do only a manual install.
2. 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.

3. Mac OS X: When Java3D is available for OS X, we will make a version of Sockeye available for this OS. See ADC.

Updates

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

Java

1. Sockeye is a Java application. Downloads are bundled with a Java3D-enabled Java Runtime (JRE 1.4.1_01). You do not need to have Java installed in order to run Sockeye. Depending on user requests, we may offer versions without a bundled JRE.
2. Linux
   1. We have tested on RedHat 7.2 and 8.0.
   2. The download file is 50+ MB. The installed application needs 73+ MB.
3. Windows
   1. We have tested on Win2K, and on XP Pro and Home.
   2. The download file is 21+ MB. The installed application needs 50+ MB.
   3. We offer installers with either DirectX or OpenGL Java3D. A comparison is available. If you have problems with one, please uninstall it and try the other.
   4. The DirectX version requires a recent version of DirectX. We have tested v0.8.3 with Microsoft's current version, (9.0a), on Win2K and XP Pro.

RAM

We have run Sockeye on PCs with between 192 MB and 1 GB of RAM. The 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

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

Source code

Source code will be made available at a later date.

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

Last modified: 2003_04_29, 18h05