It may very well be that 500MB is actually a large amount of space to sacrifice if they. But I've never really had too much of a problem with it using disk space though. I start with the base Cygwin install and add OpenSSH, Cron, RXVT, Screen. Enter the full/partial name of the missing dll to find the name of the package.

George B. Moody
Harvard-MIT Division of Health Sciences and Technology
Revised 7 November 2013

What is Cygwin?

Cygwin is freesoftware that provides a Unix-like environment and software tool setto 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 ofCygwin) some obsolete versions (95/98/ME/NT/2000/XP without SP3) aswell. Cygwin consists of a Unix system call emulationlibrary, cygwin1.dll, together witha vast set ofGNU and other free software applications organized into a large numberof optional packages. Among these packages are high-quality compilersand other software development tools, an X11 server, a complete X11development toolkit, GNU emacs, TeX and LaTeX, OpenSSH (client andserver), and much more, including everything needed to compile and usePhysioToolkit software under MS-Windows.

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

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

Installing Cygwin

Overview

Installing Cygwin begins with downloading and running the Cygwininstaller (setup-x86.exe or setup-x86_64.exe), whichis 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 ofbzip2-compressed tar (.tar.bz2) archives. The installer downloadsthese from the mirror you have chosen into a temporary directory, validatesthem by computing their MD5 sums, and then unpacks them into the rootdirectory you have chosen.

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

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

When the installation is complete, the Cygwin root directory will resemblethat 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 onthe optional packages you choose) perhaps other directories as well. Thelater sections of this page (Using Cygwin andUsing Cygwin/X) describe how to access the softwareonce it has been installed.

Prerequisites

1. Make sure that you are using a version of Windows supported by Cygwin, andthat you have sufficient disk space and time available for theinstallation, as indicated above.
2. If your Windows login name contains a space character, consider changing itor creating a separate login for use with Cygwin. The Cygwin installernames your home directory according to your Windows login name. It is usuallypossible to work around problems caused by directory or file names thatcontain spaces, but they will be a constant irritation; it's better to avoidthem.
3. Some virus scanners may interfere with Cygwin installation. If youencounter problems, consider disabling your virus scanner duringCygwin 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. Theinstallation procedure for Cygwin 1.7 has not changed significantlyfrom the procedure for Cygwin 1.5. MS-Windows 95, 98, and ME areincompatible with Cygwin 1.7; if you must use one of these olderversions of Windows, install Cygwin 1.5 (seeCygwin Legacy for instructions and download links).In-between versions (NT, 2000, XP without SP3) are compatible withversions 1.7 through 1.7.21; it is unclear if any of these versionsare currently available through the Cygwin project or the Cygwin Legacy project.

Running the Cygwin installer

1. Install Cygwin-32 now

   Click on the 'Install Cygwin-32 now' icon at right (or do so on theCygwin web site).

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

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

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

   If this happens, click 'Yes' to continue.

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

3. Choose A Download Source: Accept the default ('Install fromInternet') and click Next.
Choosing the default 'Install from Internet' causes the files youwill choose in a later step to be downloaded first and then validatedand installed. The other choices allow you to perform this procedurein two steps.

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

   Important: The default root directory for Cygwin applicationsis C:/cygwin. Change it if you wish (using '/' rather than 'as a directory separator, as shown)`, but do not choose alocation that contains spaces anywhere in its path name. Allfiles installed by the Cygwin installer go into this directory; touninstall Cygwin at a later date, simply remove this directory and allof its contents.

   Download film twilight full movie. The series is distributed by Warner Bros.

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

5. Select Local Package Directory: Accept the default(C:UsersUserDesktop) or change it to any temporarydirectory of your choice, but make a note of it.

   After the installation is complete, you may delete the .tar.gzpackage files that will have been written there. If you have chosen a fullinstallation, these files may occupy over a gigabyte, and they are nolonger needed once their contents have been installed. If you plan toinstall Cygwin on another PC, however, you may be able to save timeby copying the local package directory and the Cygwin installer to the secondPC; follow these instructions to install Cygwin on the second PC, but choose'Install from Local Directory' in step 3.

6. Select Your Internet Connection: The default should be correct formost users. Change it only if you encounter problems.

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

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

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

   The drama has a colourful look to it and while it revolves around the love stories between two young couples, Humayun Saeed’s humorous dialogues make it a treat to watch.‘TUM SE MIL KAR’ — ‘Tum Se Mil Kar’ was a serious drama released in early 2000s starring Vaneeza Ahmad and Jia Ali. In this drama, the role of the doctor was performed by Ahmad. What makes its story typical of Moin is that it discusses the ups and downs in the life of a doctor such as in ‘Dhoop Kinare’ and ‘The Castle’. Starring Asif Raza Mir, Rabi Pirzada, Tipu Sharif, Angeline Malik and Shameem Hilali, the serial is a historical one discussing the oppression of females in Sindh simultaneously. ‘MERE DARD KO JO ZUBAN MILE’ — Although a big production of PTV, this serial is not much remembered.

9. If you wish to do a custom installation, click the Viewbutton 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 theNew column) to cycle through the available choices until a versionnumber appears. In most cases, you should choose the highest version numberfrom those that are available (this is usually the first alternative offered).

   In the example below, the sunrpc package, version 4.0-2, has beenselected 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 ofthe 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 wouldalso like to download the sources for the package.

   If you plan to use PhysioToolkit software, be sure to choose at least thefollowing 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 thesethree 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 notedabove, it is not possible to use 64-bit Cygwin to build or run WAVE or otherXView-based software.)

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

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

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

    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 theload on the Cygwin mirror site from which you are downloading).

11. Once all selected package files have been downloaded and checked, they areunpacked into the Cygwin root install directory.

12. Following package installation, any installation-dependent configurationscripts are run to complete the setup process. (There may be lengthy pausesduring this step, without any indication of progress. Be patient!)

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

    These do not necessarily mean that affected packages will fail to functionproperly, 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 listof scripts that returned errors appears below the note.Click Next to continue.

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

    That's all!

You may always run Cygwin setup again to obtain additional or updated packageswithout reinstalling packages that remain current; if you do this, be sure toshut down any running Cygwin applications first.

Using Cygwin

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

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

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

Finding Cygwin files with Windows applications, and vice versa

Pathnames of files are often confusing to new Cygwin users. A pathname issimply a set of directions for finding a file. An absolute pathnamebegins at a fixed location (the root of the file system). Theconfusion arises because native Windows programs use c: as theirroot, and Cygwin programs use c:cygwin (unless you chose some otherplace 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 asc:cygwinhomebobfoo.txt (the two pathnames refer to the samedisk file).

If you need to use a Cygwin program to read or write a file located outsideof c:cygwin, you can use a pathname beginning with/cygdrive/c/ for this purpose. For example, a native Windows filecalled c:My Documentshello.c can be found by a Cygwin program at/cygdrive/c/My Documents/hello.c (note how the space characterin 'My Documents' must be prefixed by ' to force it to be treated as partof 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 frequentexample is makefile and Makefile). Be careful: althoughWindows does preserve the original case of characters in filenames, it ignorescase when looking for matches to file names. So, for example, if you writea file called baz.zip and then another called Baz.zip, thefirst one will be overwritten. This behavior might be no surprise to Windowsusers, but it may be unexpected to Unix users.

Using Cygwin/X

The X Window System, version 11 (often 'X11', or simply 'X') is the standardgraphical environment under Unix and GNU/Linux; it is also available for otherplatforms, including Mac OS X and MS-Windows. X applications ('clients')exchange data with an X server (another application). The X server receivesand interprets instructions from the clients for displaying the clients'windows, and it collects and transmits keyboard and mouse input events to theclients. 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 clientsthat run under MS-Windows.

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

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

On Cygwin 1.7, startxwin is /usr/bin/startxwin.exe,and it must be started from a Cygwin window (not a DOS box or adesktop shortcut). On Cygwin 1.5, startxwinis c:cygwinusrX11R6binstartxwin.bat, and if you create adesktop shortcut to this batch file, you can click on it to launchXwin.

If you prefer, you can run the command startx in a Cygwin window tolaunch Xwin; using this method, Xwin opens a root window on the desktop, andall 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 theGNU bash shell. An important difference is that you can launch otherX clients from an xterm without additional preparation.

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

While the X server is running, its icon ('X') appears in the Windows systemtray (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 shouldexit from all X clients before stopping the server.

Further Reading

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

Those who are new to Unix may find the additional resources listed belowto be helpful while they are becoming familiar with the Unix way of doingthings, which is quite different from the MS-Windows model. Almost anythingyou learn while using Cygwin is directly transferrable to GNU/Linux. Ifyour experience encourages you to make the leap to GNU/Linux, you mightwant to start with a live CD distribution such asKnoppix, which allowsyou to run a full GNU/Linux distribution without writing anything to yourhard disk.

• Cygwin Documentation. The Cygwin project maintains several useful documents here, including:
  • Cygwin PackageList. Look here to see if your favorite GNU/Linux application isavailable as a Cygwin package.

• UNIX Tutorial for Beginners. Although written for UNIX,almost all of this excellent tutorial from the University of Surrey isapplicable to Cygwin. The final section (tutorial 8) describes features ofcsh, an alternative to bash.

• The LinuxTerminal - a Beginner's Bash. This clearly written guide from the MaltaLinux Users' Group covers some of the same material as the previous resource,and fills in the gaps with discussion of the bash shell. Skip thesections about creating a user account and how to access the terminal window,which are GNU/Linux-specific; the remainder is a gentle introduction tobash and to the organization of a typical Unix file system (which isan accurate description of the Cygwin root directory hierarchy with theexception of /dev, which is not present under Cygwin).

• -h or --help. These command-line options areinterpreted by most Unix applications as a request for a usage summary; theyare the Unix equivalents of /?. For example, type 'mkdir--help' at a bash prompt to get a usage summary for themkdir command. Usage summaries are usually very brief and are mostuseful to help recall information you have learned from some other source.

• man pages. These are thestandard, (almost) universally available, cryptically concise, on-linereference documents for Unix programs. Type 'man program' ata bash prompt to see the man page forprogram. McGill University maintains agentle introduction to reading man pages (this seems to beoff-line as of early 2008; another introduction to man pagesis here).

• Google is your friend!One of the most efficient ways to get help with common Unix questions isby using the name of a command or the text of an error message as a Googlesearch term.

• Cygwin mailing lists and unofficial newsgroups can also be useful sources of information.