WFDB quick start for GNU/Linux

1. Install gcc (requires root permissions) if it is not installed already (try the command 'gcc --version' to check).
   
   
2. Install an HTTP client library (optional, requires root permissions) if one is not installed already (try the commands 'curl-config --version' and 'libwww-config --version' to check). If either command works, skip to step 3.

   If neither libcurl nor libwww has been installed already, install one of them now.

   • You will be able to use the WFDB software to read files on local disk drives and CD-ROMs whether or not you install one of these libraries.
   • Direct access from WFDB applications to data files on remote web and FTP servers (NETFILES) is possible only if you install libcurl or libwww.
   • Direct access from WFDB applications to password-protected data files on remote web and FTP servers requires libcurl 7.12.0 or later.
   • If you skip this step now, you may install libcurl or libwww and recompile the WFDB library later to enable NETFILES access for all of your WFDB applications. It will not be necessary to recompile the applications themselves.
   
   
3. Install the X11 developer's toolkit and XView (optional, requires root permissions) if they are not already installed. (Check for the presence of Xlib.h, which is usually found in /usr/include/X11, to see if the X11 developer's toolkit has been installed. Check for the presence of textedit, which is usually found in /usr/openwin/bin, to see if XView has been installed.)
   • You will not be able to compile or use WAVE unless you have installed the X11 developer's toolkit and XView, but none of the other WFDB applications require XView. Other components of PhysioToolkit, such as plt and SEMIA, require X11 and XView.
   • The X11 developer's toolkit is contained in a package named libX11-devel in most current GNU/Linux distributions, such as Fedora 5 and later. In some older GNU/Linux distributions, the package you need may be called xorg-x11-devel or XFree86-devel.
   • PhysioNet's XView pages contain sets of XView RPMs and instructions for installing them. Be sure to install not only the basic xview package, but also the xview-clients and xview-devel packages.
   • Add /usr/openwin/bin (or the directory containing textedit, if you have a non-standard installation of XView) to your PATH before attempting to compile WAVE.
   
   
4. Download the current version of the WFDB software package as sources or binaries. Binary packages are provided as a convenience and may not be up-to-date; we strongly recommend following the procedure described below for compiling the software from the sources instead. If you plan to compile WFDB applications that are not included in the binary package, please start with the sources.

   If you download the sources (recommended):

   • Unpack the archive of sources:

     tar xfvz wfdb.tar.gz
     

     This creates a directory with a name of the form wfdb-10.m.n.
   • Enter this directory, configure, and install the package:

     cd wfdb-10.m.n
     ./configure
     make install
     

     The make command requires root permissions, and installs the package in subdirectories of /usr. If you do not have root permissions, you may install the package in any writable directory by adding an appropriate option to the make command above:

     make install WFDBROOT=/path/to/another/directory
     

     Note that in this case you will need to add WFDBROOT/bin to your PATH, and WFDBROOT/lib to your LD_LIBRARY_PATH.
   • (Optional) Check that the WFDB library and applications have been correctly compiled and installed:

     make check
     

     This step compiles a short program that exercises the WFDB library, prints a summary of test results, and prompts you to press <Enter>. After you have done so, the WFDB applications are tested. The tests are very short (typically less than a second each), except that the last one (xform using NETFILES) may take up to a minute if you have a slow or inoperative Internet connection. If any application test fails, its output can be found in the checkpkg subdirectory of the WFDB source tree; compare this output with the files of the same names that can be found in the checkpkg/expected subdirectory.
   
   If you download the binaries (not recommended):
   • If you have the RPM utility, and have installed libcurl and XView, download the binary WFDB RPMs for your distribution from the directory of Linux binaries, and install them:

              rpm -Uvh wfdb*rpm
     	 /sbin/ldconfig
            

   • Otherwise, look for wfdb-10.m.n in the directory of Linux binaries. Within wfdb-10.m.n you will find bin and lib directories. Copy the files from the lib directory into one of the directories named in /etc/ld.so.conf (/usr/lib is recommended) and run /sbin/ldconfig (requires root permissions). Next, copy the applications from the bin directory into any directory in your PATH.
   
   
5. If XView is installed, test WAVE with the command:

   wave -r mitdb/200 -a atr
   

   If you have not used WAVE before, you may want to follow through the tutorial material in the beginning of the WAVE User's Guide.
   
   
6. Read the manuals. Really! :-) If you want to write your own software to work with PhysioBank data, begin with the WFDB Programmer's Guide. To learn about the wide variety of existing software that can be used to study PhysioBank data, read the WFDB Applications Guide and the WAVE User's Guide.

Your comments and suggestions are welcome. We encourage you to use our feedback form to comment on this page. If you would like to receive a reply, please send your comments by email to webmaster@physionet.org, or post them to: PhysioNet MIT Room E25-505A 77 Massachusetts Avenue Cambridge, MA 02139 USA

Updated Wednesday, 05-Sep-2007 12:18:37 EDT