An Introduction to Cygwin

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George B. Moody
Harvard-MIT Division of Health Sciences and Technology

Revised 7 November 2013

What is Cygwin?

Cygwin is free software that provides a Unix-like environment and software tool set to users of any modern x86 32-bit and 64-bit versions of MS-Windows (XP with SP3/Server 20xx/Vista/7/8) and (using older versions of Cygwin) some obsolete versions (95/98/ME/NT/2000/XP without SP3) as well. Cygwin consists of a Unix system call emulation library, cygwin1.dll, together with a vast set of GNU and other free software applications organized into a large number of optional packages. Among these packages are high-quality compilers and other software development tools, an X11 server, a complete X11 development toolkit, GNU emacs, TeX and LaTeX, OpenSSH (client and server), and much more, including everything needed to compile and use PhysioToolkit software under MS-Windows.

Cygwin does not provide a means for running GNU/Linux or other Unix binary executables under MS-Windows. In order to run such software using Cygwin, that software must be compiled from its sources. Cygwin provides all of the components needed to do this in most cases; most POSIX-compliant software, including X11 applications, can easily be ported to MS-Windows using Cygwin.

This page is provided as a service to help PhysioNet users and others get started using Cygwin. PhysioNet and the author are unaffiliated with the Cygwin project and cannot assist users in installing and using Cygwin. For general assistance on Cygwin beyond what is included here, please use the resources listed at the end of the page.

Installing Cygwin


Installing Cygwin begins with downloading and running the Cygwin installer (setup-x86.exe or setup-x86_64.exe), which is a small application that allows you to choose:

as well as a few other installation options. Cygwin packages consist of bzip2-compressed tar (.tar.bz2) archives. The installer downloads these from the mirror you have chosen into a temporary directory, validates them by computing their MD5 sums, and then unpacks them into the root directory you have chosen.

If you have at least 30 Gb free disk space (roughly half of which can be reclaimed after installation), you may choose to perform a full installation of Cygwin with all of its optional packages. This choice is recommended for those who prefer to work in a Unix or GNU/Linux environment but who are constrained to work under MS-Windows. A full installation provides a large subset of the software provided as standard components of a typical GNU/Linux distribution. Allow at least an hour to perform a full installation if you have a fast Internet connection, more otherwise.

If you wish only to compile and use existing software under MS-Windows, you may choose a custom installation of Cygwin, consisting of the Base package and a few optional packages listed below; this choice requires less than 1 Gb, and proportionately less time than a full installation. A minimal installation may be upgraded easily at a later time, by following the same procedure as for initial installation. Packages that have previously been installed will not be changed unless newer versions have become available and you choose to install them.

When the installation is complete, the Cygwin root directory will resemble that of a typical Unix or GNU/Linux system, with subdirectories bin (applications and DLLs), etc (configuration files), home (containing a subdirectory for each Windows user registered on your system), lib (static libraries), tmp (temporary files), usr (containing additional software), var (log files), and (depending on the optional packages you choose) perhaps other directories as well. The later sections of this page (Using Cygwin and Using Cygwin/X) describe how to access the software once it has been installed.


  1. Make sure that you are using a version of Windows supported by Cygwin, and that you have sufficient disk space and time available for the installation, as indicated above.
  2. If your Windows login name contains a space character, consider changing it or creating a separate login for use with Cygwin. The Cygwin installer names your home directory according to your Windows login name. It is usually possible to work around problems caused by directory or file names that contain spaces, but they will be a constant irritation; it's better to avoid them.
  3. Some virus scanners may interfere with Cygwin installation. If you encounter problems, consider disabling your virus scanner during Cygwin installation and re-enabling it afterwards.

Cygwin 1.5.x vs. Cygwin 1.7.x

Cygwin 1.7 is the current version as of December 2009. The installation procedure for Cygwin 1.7 has not changed significantly from the procedure for Cygwin 1.5. MS-Windows 95, 98, and ME are incompatible with Cygwin 1.7; if you must use one of these older versions of Windows, install Cygwin 1.5 (see Cygwin Legacy for instructions and download links). In-between versions (NT, 2000, XP without SP3) are compatible with versions 1.7 through 1.7.21; it is unclear if any of these versions are currently available through the Cygwin project or the Cygwin Legacy project.

Running the Cygwin installer

  1. Cygwin!
    Click on the "Install Cygwin-32 now" icon at right (or do so on the Cygwin web site).

    Save the link (setup-x86.exe) to your desktop, then double-click on the saved icon to begin installation.

    If you prefer, you may install Cygwin-64 using the setup-x86-64.exe installer from the Cygwin web site. Note that XView-based software from PhysioToolkit, including WAVE, cannot be compiled on Windows using 64-bit Cygwin, since several required DLLs are available in 32-bit versions only.

    A window titled User Account Control may appear, with the question

        Do you want to allow the following program from an unknown publisher
        to make changes to this computer?
           Program name: setup.exe
           Publisher:    Unknown
           File origin:  Downloaded from the Internet

    If this happens, click "Yes" to continue.

  2. A window titled Cygwin Net Release Setup Program appears. Click Next to get started.

    [Cygwin installer]

  3. Choose A Download Source: Accept the default ("Install from Internet") and click Next.

    [Choose A Download Source]

  4. Choosing the default "Install from Internet" causes the files you will choose in a later step to be downloaded first and then validated and installed. The other choices allow you to perform this procedure in two steps.

  5. Select Root Install Directory: Accept the defaults ("C:/cygwin", All Users, Unix) and click Next.

    [Select Root Install Directory]

    Important: The default root directory for Cygwin applications is C:/cygwin. Change it if you wish (using '/' rather than '\' as a directory separator, as shown)`, but do not choose a location that contains spaces anywhere in its path name. All files installed by the Cygwin installer go into this directory; to uninstall Cygwin at a later date, simply remove this directory and all of its contents.

    If you are installing Cygwin 1.7, you won't see an option to choose the default text file type. If you are installing Cygwin 1.5, you will have a choice as shown above, but don't change the default text file type ("Unix").

  6. Select Local Package Directory: Accept the default (C:\Users\User\Desktop) or change it to any temporary directory of your choice, but make a note of it.

    [Select Local Package Directory]

    After the installation is complete, you may delete the .tar.gz package files that will have been written there. If you have chosen a full installation, these files may occupy over a gigabyte, and they are no longer needed once their contents have been installed. If you plan to install Cygwin on another PC, however, you may be able to save time by copying the local package directory and the Cygwin installer to the second PC; follow these instructions to install Cygwin on the second PC, but choose "Install from Local Directory" in step 3.

  7. Select Your Internet Connection: The default should be correct for most users. Change it only if you encounter problems.

    [Cygwin installer]

  8. Choose A Download Site: Select a nearby mirror site from which to download the Cygwin packages. Speeds may vary considerably from site to site.

    [Cygwin installer]

    At this time, the installer downloads a list of available packages from the site you have chosen. Normally, this takes only a few seconds; if there is a lengthy pause, you may wish to start over and choose a different mirror site.

  9. Select Packages: If you wish to do a full installation, click on the rotating selector next to "All" (at the top of the Category list) so that the indicator to its right changes from "Default" to "Install". Click Next and skip ahead to step 10.

    [Cygwin installer]

  10. If you wish to do a custom installation, click the View button so that the indicator to its right changes from "Category" to "Full".

    [Cygwin installer]

    If you are installing Cygwin 1.5, the dialog box may be too small initially; you may resize it as needed until the package names are visible.

    To select a package for installation, click on its rotating selector (in the New column) to cycle through the available choices until a version number appears. In most cases, you should choose the highest version number from those that are available (this is usually the first alternative offered).

    [Cygwin installer]

    In the example below, the sunrpc package, version 4.0-2, has been selected for installation. Note that the entry in the Bin? (Binary) column changes from n/a to a checked box when you select a numbered version of the package. Leave this box checked. The entry in the Src? (Source) column changes from n/a to an unchecked box, which you may check if you would also like to download the sources for the package.

    [Cygwin installer]

    If you plan to use PhysioToolkit software, be sure to choose at least the following packages for installation:

    • ImageMagick (Graphics)
    • bc (Math, Utils)
    • curl (Net, Web)
    • cygutils-extra (Utils)
    • diffutils (Utils)
    • gcc (Devel)
    • gcc-fortran (Devel)
    • gv (Graphics, Text, X11)
    • libX11-devel (X11)
    • libcurl-devel (Devel, Net, Web; curl-devel in Cygwin 1.5)
    • libexpat-devel (X11)
    • make (Devel)
    • mingw-gcc (Devel; gcc-mingw in Cygwin 1.5)
    • twm (X11)

    In addition, if you are installing a 32-bit version of Cygwin, choose these three packages that are needed by XView-based software such as WAVE:

    • X-start-menu-icons (X11)
    • sunrpc (Libs)
    • xview-devel (X11)

    (These packages are not available for 64-bit versions of Cygwin, and, as noted above, it is not possible to use 64-bit Cygwin to build or run WAVE or other XView-based software.)

    The categories to which each package belongs are shown following the package names above, for reference. You may choose any other desired packages, either at this time or later on (by running Cygwin setup again). The Cygwin installer will automatically download any additional packages needed to satisfy dependencies of those you select. When you have completed your selections, click Next.

  11. On Cygwin 1.7, setup may show a window with a warning ("Resolving Dependencies") and a list of additional packages required by those you have already selected. At the bottom of the window, be sure that "Select required packages (RECOMMENDED)" is checked, then click Next.

    The downloading process begins once the packages have been selected. The installer indicates its progress.

    [Cygwin installer]

    Be patient; the downloading and installation process may take an hour or more (depending not only on the speed of your Internet connection, but also on the load on the Cygwin mirror site from which you are downloading).

  12. Once all selected package files have been downloaded and checked, they are unpacked into the Cygwin root install directory.

    [Cygwin installer]

  13. Following package installation, any installation-dependent configuration scripts are run to complete the setup process. (There may be lengthy pauses during this step, without any indication of progress. Be patient!)

    [Cygwin installer]

    A window titled Postinstall script errors may appear after all of the configuration scripts have been run. If so, it contains an explanatory note:

    These do not necessarily mean that affected packages will fail to function properly, but please check /var/log/setup.full and report any problems.

    The name of the file is /var/log/setup.log (not /var/log/setup.full). Report any problems to the Cygwin project, not to PhysioNet! A list of scripts that returned errors appears below the note. Click Next to continue.

  14. Create Icons: Unless these icons already exist from a previous Cygwin installation, make sure the boxes are checked and click Finish.

    [Cygwin installer]

    That's all!

You may always run Cygwin setup again to obtain additional or updated packages without reinstalling packages that remain current; if you do this, be sure to shut down any running Cygwin applications first.

Using Cygwin

As noted, Cygwin provides a Unix-like environment under Windows. The installation directory (by default, c:\cygwin) is the root of the Unix-like file system, which contains bin, etc, home, tmp, and usr directories as would be found on a GNU/Linux or other Unix system. Within home will be one or more subdirectories, each allocated to a Windows user.

Cygwin desktop icon

To begin, click on the Cygwin desktop icon, or choose the Cygwin entry from your start menu, to open a Cygwin terminal window. Within this window, the GNU bash shell is running, with POSIX syntax (directory separators are '/', not '\'). Initially, the current (working) directory is /home/user, where user is your Windows login name. Don't use this directory if your Windows login name contains a space; make another and use that one instead, e.g., by typing these commands at the bash prompt:

    mkdir /home/bob
    echo "export HOME=/home/bob" >>.bashrc
    echo "export HOME=/home/bob" >>.bash_profile
    cp .bashrc .bash_profile /home/bob
    echo "cd" >>.bashrc

Close your Cygwin terminal window and open another one; your current directory should now be /home/bob (or whatever you chose to call it). See the Cygwin FAQ (look for "My Windows logon name has a space in it") for other solutions to this common problem.

Finding Cygwin files with Windows applications, and vice versa

Pathnames of files are often confusing to new Cygwin users. A pathname is simply a set of directions for finding a file. An absolute pathname begins at a fixed location (the root of the file system). The confusion arises because native Windows programs use c:\ as their root, and Cygwin programs use c:\cygwin (unless you chose some other place to install Cygwin).

This means, for example, that a file created using a Cygwin program as /home/bob/foo.txt can be read using a native Windows program as c:\cygwin\home\bob\foo.txt (the two pathnames refer to the same disk file).

If you need to use a Cygwin program to read or write a file located outside of c:\cygwin, you can use a pathname beginning with /cygdrive/c/ for this purpose. For example, a native Windows file called c:\My Documents\hello.c can be found by a Cygwin program at /cygdrive/c/My\ Documents/hello.c (note how the space character in "My Documents" must be prefixed by "\" to force it to be treated as part of the pathname). If you have a Windows d: drive, use /cygdrive/d/ in the same way to access its contents from Cygwin programs.

Unix/Linux files occasionally have names that differ only in case (a frequent example is makefile and Makefile). Be careful: although Windows does preserve the original case of characters in filenames, it ignores case when looking for matches to file names. So, for example, if you write a file called and then another called, the first one will be overwritten. This behavior might be no surprise to Windows users, but it may be unexpected to Unix users.

Using Cygwin/X

The X Window System, version 11 (often "X11", or simply "X") is the standard graphical environment under Unix and GNU/Linux; it is also available for other platforms, including Mac OS X and MS-Windows. X applications ("clients") exchange data with an X server (another application). The X server receives and interprets instructions from the clients for displaying the clients' windows, and it collects and transmits keyboard and mouse input events to the clients. The xorg packages available with Cygwin (collectively, "Cygwin/X") provide a high-quality X server, a large set of standard X clients, and a complete set of development tools that can be used to compile X clients that run under MS-Windows.

Important: X clients cannot run unless they can connect to a running X server. The X server must be started first. When you use Cygwin/X, its X server (Xwin) runs on your PC, under MS-Windows. Once Xwin is running, you can launch and interact with X clients on your PC or on any other networked computer (which can be running MS-Windows, GNU/Linux, Mac OS X, Unix, or any other OS that can run X client software).

Since Xwin is a complete window system, it has a "root" (background) window on which X clients' windows are displayed. Xwin can run in "rootless" mode, in which its root window is invisible, allowing the MS-Windows desktop and application windows to be visible, and allowing the X clients' windows to be moved, resized, closed, and reopened using the same methods as for native MS-Windows applications. Use startxwin to run Xwin in rootless mode.

On Cygwin 1.7, startxwin is /usr/bin/startxwin.exe, and it must be started from a Cygwin window (not a DOS box or a desktop shortcut). On Cygwin 1.5, startxwin is c:\cygwin\usr\X11R6\bin\startxwin.bat, and if you create a desktop shortcut to this batch file, you can click on it to launch Xwin.

If you prefer, you can run the command startx in a Cygwin window to launch Xwin; using this method, Xwin opens a root window on the desktop, and all X client windows are contained within Xwin's root window.

When you launch Xwin, it starts an xterm (terminal emulator) client:


Within this window, just as in a Cygwin terminal window, you are running the GNU bash shell. An important difference is that you can launch other X clients from an xterm without additional preparation.

You can access xterm's menus by pressing and holding the Ctrl key while clicking the left, middle, or right mouse buttons. Use these menus to enable the scrollbar (as shown in the screen shot above) or to change the character size, among other possibilities.

While the X server is running, its icon ("X") appears in the Windows system tray (see above). You can click on this icon to force the X server to exit, but doing so will also force any X clients to exit; normally you should exit from all X clients before stopping the server.

Further Reading

Readers who are familiar with GNU/Linux or Unix may not need much more information than what is given above to begin using Cygwin productively. The environment is so Unix-like that it's easy to forget that it is all running under MS-Windows. The Cygwin project documentation highlights the important differences between Cygwin and other Unix(-like) environments.

Those who are new to Unix may find the additional resources listed below to be helpful while they are becoming familiar with the Unix way of doing things, which is quite different from the MS-Windows model. Almost anything you learn while using Cygwin is directly transferrable to GNU/Linux. If your experience encourages you to make the leap to GNU/Linux, you might want to start with a live CD distribution such as Knoppix, which allows you to run a full GNU/Linux distribution without writing anything to your hard disk.

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Updated Tuesday, 17 April 2018 at 18:24 EDT

PhysioNet is supported by the National Institute of General Medical Sciences (NIGMS) and the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number 2R01GM104987-09.