Linux Install Information
We install the Linux@Duke version of Fedora Core 4 on Linux workstations.
Core installed packages
"X" means the the group of applications is installed.
[X] X window System [X] GNOME Desktop [X] KDE (K Desktop Environment) [X] Editors [X] Engineering and Scientific [X] Graphical Internet [X] Text-based Internet [X] Office/Productivity [X] Sound and Video [X] Authoring and Publishing [X] Graphics [ ] Games and Entertainment [X] Server Configuration Tools [X] Web Server [ ] Mail Server [ ] Windows File Server [ ] DNS Name Server [ ] News Server [ ] Network Servers [X] Development Tools [ ] Kernel Development [ ] X Software Development [ ] GNOME Software Development [ ] KDE Software Development [X] Administrative Tools [X] System Tools [X] Printing Support [ ] Everything
For gritty details on the packages removed, packages added, and packages that have been "deprecated" in the Fedora Core distribution see http://install.linux.duke.edu/pub/linux/base/4/i386/RELEASE-NOTES-en.html Specifics about individual packages provided by these groups is available in XML form (yumgroups.xml, 410 KB).
Please note that the only changes of Fedora Core 4 introduced in the Linux@Duke distribution have to do with the repositories for installation and updating. Otherwise Linux@Duke is Fedora Core 2.
Additional packages
In addition to the core packages, other packages are added. These have not been included in the core mainly because they are distributed under a license that doesn't meet the Fedora Project's (very stringent) requirements or the applications do not have wide enough use in the target market for the Fedora Project.
acroread acroread-plugin emacs-ess firefox galeon (deprecated) matlabR14 matlabR14-toolbox-image matlabR14-toolbox-statistics mysql perl-Bioperl pine R sunjava2 sunjava2-plugin thunderbird
(Postgresql, by the way, is the "default" database provided by Fedora Core 4, though MySQL is available as an "option."" We have installed MySQL in lieu of Postgresql.)
Other applications, mostly of a bioinformatical sort, are available through NFS mounts, described below.
The rhn-applet is removed.
If a project requires specialized software not included in the basic installation, it can be added to a machine or a set of machines or made available in another IGSP-distributed fashion.
NFS mounts
NFS is used to provide "home" directories on Linux machines. Also, commonly used applications and analysis resources are available by NFS mounts. See http://tools.genome.duke.edu/tools.php for a complete list of bioinformatic and computational biology resources. On that list, you can see the applications available by NFS mount. You do not need to "set the path" to use these resources from the command line, since the paths are included in your environment. However, if you use the NFS mounted software resources in a script, you will often need to include the entire path in the script.
A note about versions
To determine the version of an application installed on a machine, you can often use the "-v" or the "--version" parameter (e.g., "gcc -v"). If that doesn't work, version numbers are also available by entering "yum list [package-name]" at the prompt.
"Local" storage
On occasion, projects require that data or applications be stored on a specific machine. Although we discourage this and seek instead to make accommodations on a server, we can create a section of a machine's hard drive for such use. This data is not available to other machines, except through SSH access. It is also not backed up. It is best to consult with a member of the IGSP IT group to find another workable solution for a special storage need.
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