Installing OpenSSH OpenSSH is what we’ll be using, so if you don’t have it installed, find Cygwin’s setup.exe file and run it. You can keep all of the same defaults as when you originally set up Cygwin. On the package selection screen, search for “open” and look under the “Net” menu. You’ll see a package called “openssh”. Click under the “New” column, where it says “Skip” until you see an X appear in the “Bin?” column. Look at the previous screenshot for where to click if you’re confused.
Hit “Next” and finish up the rest of the setup process, just like you did last time. Configuring OpenSSH in Cygwin Unlike in most Linux distros, OpenSSH won’t automatically configure itself to run and just work. We need to perform a few easy steps. First, right-click your Cygwin shortcut, and click on “Run as administrator”: This will make sure we have the proper privileges for everything. You’ll see an empty Cygwin window come up. Enter the following command: ssh-host-config You’ll see the script generate some default files, and then you’ll be prompted for whether or not you want to enable “Privilege Separation.” It’s on by default in standard installations of OpenSSH on other systems, so go ahead and say “yes” to the prompt. You’ll be prompted to create a new account with special privileges.
Select “yes” and the script will continue. Next, you’ll be asked if you want sshd to run as a service. This will allow you to get SSH access regardless of whether or not Cygwin is currently running, which is what we want.
Go ahead and hit “yes” to continue. Next, you’ll be asked to enter a value for the daemon. Enter the following: ntsec You’ll see the script give you some information on your system and then it will ask you to create a privileged account with the default username “cygserver”.
The default works well, so type “no” when it asks you if you want to use a different account name, although you can change this if you really like. Of course, you’ll have to enter a password for this account as well. Cygwin will show you your password in plain text for verification, so be sure you’re in a secure place. You’ll see some extra info come up and if all’s well, you’ll get a message that says it successfully completed. You can either restart, or enter the following command to start the sshd service: net start sshd Now, you can type “exit” to close this Cygwin instance.
User Configuration of SSH Next, we’ll create the appropriate SSH keys for your user account. Open up Cygwin normally, and enter the following command: ssh-user-config You’ll be asked to create specific keys for your user account, so use what you need. I went ahead and said “no” to the first question, and “yes” to the second. SSH2 is more secure, so that’s what I recommend to you. After entering a password, you’ll be asked if you want to use that ID to access your machine. Next, you’ll be asked to create an SSH2 DSA ID file, if you want to use password-less access. I declined at this step.
Cygwin is free software to provide Linux and Unix environment, tools and libraries in Windows operating systems. Cygwin is also called an emulator because it translates Linux system calls into Windows type systems calls. Cygwin generally used to run Linux tools like ssh,scp,bash, X11,gcc in Windows environment. Jun 9, 2006 - Introduction to who? If that's what you thought when you saw the title of this article, then it's written for you.
You’re all configured. If you want to test your configuration really quickly, enter the following command in your Cygwin window: ssh –v localhost The –v option stands for “verbose” and gives you all of the details of the process. You’ll be asked if you want to continue connecting, so enter “yes” and then enter your password at the prompt. Remember that when you enter your username, it is case-sensitive! If everything worked out well, you’ll see a normal bash prompt. Minor Issues If you find yourself stuck at any of the configuration steps, make sure that the Windows User Account you’re running has Administrative access. You may get weird errors if you try to run the host configuration as a normal user, so make sure you run Cygwin with admin privileges during that step.
If, when you exit, you get a prompt about leaving your batch jobs running, you can hit “no” to terminate them. Lastly, if you test SSH access from another machine and get an error, make sure that your firewall isn’t blocking access to port 22 (or 23 if you’re using SFTP). This works extremely well if you like the ability to get SSH/SFTP access to your files on a Windows 7 machine and you also want a familiar shell to do that with.
Cygwin mounts Windows drives to “/cygdrive/driveletter” in case you were wondering.;-).
An Introduction to Cygwin George B. Moody Harvard-MIT Division of Health Sciences and Technology Revised 7 November 2013 What is 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 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 listed at the end of the page.
Installing Cygwin Overview Installing Cygwin begins with downloading and running the Cygwin installer ( setup-x86.exe or setup-x8664.exe), which is a small application that allows you to choose:. the Cygwin root directory (where Cygwin will be installed on your system). which of the many Cygwin mirrors you will use while downloading.
which optional Cygwin packages should be installed 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 ( and ) describe how to access the software once it has been installed.
Prerequisites. 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. 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. 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 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. Click on the 'Install Cygwin-32 now' icon at right (or do so on the ). 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 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. A window titled Cygwin Net Release Setup Program appears. Click Next to get started. Choose A Download Source: Accept the default ('Install from Internet') and click Next.
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. Select Root Install Directory: Accept the defaults ('C:/cygwin', All Users, Unix) and click Next. 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'). 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.
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. Select Your Internet Connection: The default should be correct for most users. Change it only if you encounter problems.
Choose A Download Site: Select a nearby mirror site from which to download the Cygwin packages. Speeds may vary considerably from site to site. 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. 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.
If you wish to do a custom installation, click the View button so that the indicator to its right changes from 'Category' to 'Full'. 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). 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. 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'.bashprofile cp.bashrc.bashprofile /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 (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 baz.zip and then another called Baz.zip, 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 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, which allows you to run a full GNU/Linux distribution without writing anything to your hard disk. The Cygwin project maintains several useful documents here, including:.
Look here to see if your favorite GNU/Linux application is available as a Cygwin package. Although written for UNIX, almost all of this excellent tutorial from the University of Surrey is applicable to Cygwin. The final section (tutorial 8) describes features of csh, an alternative to bash. This clearly written guide from the Malta Linux Users' Group covers some of the same material as the previous resource, and fills in the gaps with discussion of the bash shell. Skip the sections about creating a user account and how to access the terminal window, which are GNU/Linux-specific; the remainder is a gentle introduction to bash and to the organization of a typical Unix file system (which is an accurate description of the Cygwin root directory hierarchy with the exception of /dev, which is not present under Cygwin).h or -help. These command-line options are interpreted by most Unix applications as a request for a usage summary; they are the Unix equivalents of /? For example, type ' mkdir -help' at a bash prompt to get a usage summary for the mkdir command.
Usage summaries are usually very brief and are most useful to help recall information you have learned from some other source. These are the standard, (almost) universally available, cryptically concise, on-line reference documents for Unix programs. Type ' man program' at a bash prompt to see the man page for program. McGill University maintains a gentle (this seems to be off-line as of early 2008; another introduction to man pages is ).
One of the most efficient ways to get help with common Unix questions is by using the name of a command or the text of an error message as a Google search term. and can also be useful sources of information.