Cygwin uses packages to manage installing various software. When the default Install from Internet option is chosen, setup.exe creates a local directory to store the packages before actually installing the contents. Download from Internet performs only the first part (storing the packages locally), while Install from Local Directory performs only the second (installing the contents of the packages).

The Download from Internet option is mainly for creating a base Cygwin package tree on one computer for installation on several machines with Install from Local Directory; copy the entire local package tree to another machine with the directory tree intact. For example, you might create a C:\cache\ directory and place setup.exe in it. Run setup.exe to Install from Internet or Download from Internet, then copy the whole C:\cache\ to each machine and instead choose Install from Local Directory. Unfortunately setup.exe does not yet support unattended installs.

Though this provides some basic mirroring functionality, if you are managing a wide Cygwin installation, to keep up to date we recommend using a mirroring tool such as wget. A helpful user on the Cygwin mailing list created a simple demonstration script to accomplish this; search the list for mkcygwget for ideas.

The Root Directory for Cygwin (default C:\cygwin) will become / within your Cygwin installation. You must have write access to the parent directory, and any ACLs on the parent directory will determine access to installed files.

The Install For options of All Users or Just Me should always be left on the default All Users, unless you do not have write access to HKEY_LOCAL_MACHINE in the registry or the All Users Start Menu. This is true even if you are the only user planning to use Cygwin on the machine. Selecting Just Me will cause problems for programs such as crond and sshd. If you do not have the necessary permissions, but still want to use these programs, consult the Cygwin mailing list archives about others' experiences.

The Default Text File Type should be left on Unix (that is, \n) unless you have a very good reason to switch it to DOS (that is, \r\n).

The Local Package Directory is the cache where setup.exe stores the packages before they are installed. The cache must not be the same folder as the Cygwin root. Within the cache, a separate directory is created for each Cygwin mirror, which allows setup.exe to use multiple mirrors and custom packages. After installing Cygwin, the cache is no longer necessary, but you may want to retain the packages as backups, for installing Cygwin to another system, or in case you need to reinstall a package.

The Direct Connection method of downloading will directly download the packages, while the IE5 method will leverage your IE5 cache for performance. If your organisation uses a proxy server or auto-configuration scripts, the IE5 method also uses these settings. If you have a proxy server, you can manually type it into the Use Proxy section. Unfortunately, setup.exe does not currently support password authorization for proxy servers.

Since there is no way of knowing from where you will be downloading Cygwin, you need to choose at least one mirror site. Cygwin mirrors are geographically distributed around the world; check the list at http://cygwin.com/mirrors.html to find one near you. You can select multiple mirrors by holding down CTRL and clicking on each one. If you have the URL of an unlisted mirror (for example, if your organization has an internal Cygwin mirror) you can add it.

For each selected mirror site, setup.exe downloads a small text file called setup.bz2 that contains a list of packages available from that site along with some basic information about each package which setup.exe parses and uses to create the chooser window. For details about the format of this file, see the setup.exe homepage.

The chooser is the most complex part of setup.exe. Packages are grouped into categories, and one package may belong to multiple categories (assigned by the volunteer package maintainer). Each package can be found under any of those categories in the heirarchial chooser view. By default setup.exe will install only the packages in the Base category and their dependencies, resulting in a minimal Cygwin installation. However, this will not include many commonly used tools such as gcc (which you will find in the Devel category). Since setup.exe automatically selects dependencies, be careful not to unselect any required packages. In particular, everything in the Base category is required.

You can change setup.exe's view style, which is helpful if you know the name of a package you want to install but not which category it is in. Click on the View button and it will rotate between Category (the default), Full (all packages), and Partial (only packages to be upgraded). If you are familiar with Unix, you will probably want to at least glance through the Full listing for your favorite tools.

Once you have an existing Cygwin installation, the setup.exe chooser is also used to manage your Cygwin installation. Information on installed packages is kept in the /etc/setup/ directory of your Cygwin installation; if setup.exe cannot find this directory it will act just like you had no Cygwin installation. If setup.exe finds a newer version of an installed package available, it will automatically mark it to be upgraded. To Uninstall, Reinstall, or get the Source for an existing package, click on Keep to toggle it. Also, to avoid the need to reboot after upgrading, make sure to close all Cygwin windows and stop all Cygwin processes before setup.exe begins to install the upgraded package.

The final feature of the setup.exe chooser is for Previous and Experimental packages. By default the chooser shows only the current version of each package, though mirrors have at least one previous version and occasionally there is a testing or beta version of a package available. To see these package, click on the Prev or Exp radio button. Be warned, however, that the next time you run setup.exe it will try to replace old or experimental versions with the current stable version.

First, setup.exe will download all selected packages to the local directory chosen earlier. Before installing, setup.exe performs a checksum on each package. If the local directory is a slow medium (such as a network drive) this can take a long time. During the download and installation, setup.exe show progress bars for the current task and total remaining disk space.

You may choose to install shortcuts on the Desktop and/or Start Menu to start a bash shell. If you prefer to use a different shell or the native Windows version of rxvt, you can use these shortcuts as a guide to creating your own.

Last of all, setup.exe will run any post-install scripts to finish correctly setting up installed packages. Since each script is run separately, several windows may pop up. If you are interested in what is being done, see the Cygwin Package Contributor's Guide at http://cygwin.com/setup.html When the last post-install script is completed, setup.exe will display a box announcing the completion. A few packages, such as the OpenSSH server, require some manual site-specific configuration. Relevant documentation can be found in the /usr/doc/Cygwin/ or /usr/share/doc/Cygwin/ directory.

Unfortunately, the complex setup process means that odd problems can occur. If you're having trouble downloading packages, it may be network congestion, so try a different mirror and/or a different protocol (i.e., HTTP instead of FTP). If you notice something is not working after running setup, you can check the setup.exe log file at /var/log/setup.log.full. Make a backup of this file before running setup.exe again, and follow the steps for Reporting Problems with Cygwin.