Home >> Madeline 2.0 Installation Instructions

Madeline 2.0 PDE Installation Instructions

Madeline is distributed primarily in source code form. Installation therefore normally requires building Madeline on your own computer. Even if you plan on building Madeline on Apple OS X or Windows, please familiarize yourself with the directions for Linux first, as the procedure is very similar on all platforms, and for the other platforms I will primarily point out where things are different from Linux rather than repeating every detail from the Linux section.

Jump to installation directions for:

Linux (recommended reading!)
Macintosh OS X
Windows

Linux and Similar Systems

Introduction

It is straightforward to build Madeline 2.0 PDE on a modern Linux and similar Unix- or Unix-like systems such as Mac OSX. These instructions assume that you have basic familiarity with installing software, including installation from source packages, on Linux and similar systems.

Software package management varies by Linux distribution. Examples of binary package installation shown below are based on Ubuntu because Ubuntu is an extremely popular distribution of Linux and the Debian-based Advanced Packaging Tool ("apt") is robust, convenient, and easy to use. Procedures for other distributions will be comparable. For example, on Mac OSX you might use the Macports toolset, in which case you would use the "port" tool in place of "apt". Consult your system documentation as required.

Prerequisites

Make sure that you have the following installed on your system:

Standard Linux development tools are needed to build Madeline from source. This includes the GCC compiler, GNU make, a linker, and others. If you are unfamiliar with these tools and procedures, consider taking some time to read this introduction to installing software from source in Linux or this introduction to development on Linux.
The Git source code management tool is needed to checkout the latest Madeline source code tree. The command-line tool, git, should be available on modern Linux distributions:

  # apt-get install git

CMake is a modern cross-platform build system used by Madeline. If you are using an older distribution of Linux, you might need to upgrade to the latest version of CMake before attempting to build Madeline. If you are using Ubuntu or a similar debian-based system, you would upgrade cmake as root using the following command:

  # apt-get install cmake

OpenSSL implements the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. The SSL library is used by LibCurl (below) to provide HTTPS (hypertext transfer protocol over secure sockets). While your Linux system almost certainly already has an installed SSL library, it is worthwhile to check that you have the latest version. It is critical to have the development package installed so that LibCurl will have access to the header files needed for compilation. If you are using Ubuntu or a similar debian-based system, you can, as root, upgrade to the latest development package using the following command:

  # apt-get install libssl-dev

LibCurl is an OpenSource library which provides network services such as HTTP and HTTPS. Madeline uses LibCurl to read files over the network. LibCurl is present on modern Linux systems, but you might have to install the development version of LibCurl which includes the header files. For example, on Ubuntu as root you would execute the following command to install the development files needed when using LibCurl:

  # apt-get install libcurl-dev

libXML2 is an Open Source library for parsing XML. Madeline uses libXML2 to parse many of the data files that it recognizes. LibXML2 is present on modern Linux systems, but you still might have to install the development version of LibXML2 which includes the header files. Using Ubuntu as an example again, the installation command would look like this:

  # apt-get install libxml2-dev

Optional

DOxygen is a source code documentation system. Make sure you have this tool if you plan to look at the source code for Madeline.

  # apt-get install doxygen

OK, we are now ready to build the software:

Step 1: Get the source

Check out the latest source code using git:

~> git clone https://github.com/piratical/Madeline_2.0_PDE.git
Cloning into 'Madeline_2.0_PDE'...
remote: Counting objects: 1743, done.
remote: Total 1743 (delta 0), reused 0 (delta 0), pack-reused 1743
Receiving objects: 100% (1743/1743), 3.15 MiB | 3.72 MiB/s, done.
Resolving deltas: 100% (829/829), done.
Checking connectivity... done.

Step 2: Configure

Go into the Madeline directory and run cmake . (the dot "." is important!). Alternatively, you can just type ./configure which will run cmake for you:

~> cd Madeline_2.0_PDE/
~> cmake .
-- Check for working C compiler: /usr/local/bin/gcc
-- Check for working C compiler: /usr/local/bin/gcc -- works
-- Check size of void*
-- Check size of void* - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
   ...
-- === NOTA BENE: === Madeline will be installed in /usr/local
-- Configuring done
-- Generating done
-- Build files have been written to: /home/edtrager/madeline2/madeline2/trunk
~>

Step 3: Build

Run make:

~> make
      ...
Generating docs for file XMLTagManager.h...
Generating class documentation...
Generating annotated compound index...
Generating hierarchical class index...
Generating member index...
Generating docs for compound Affected...
Generating docs for compound AffectedMapLoader...
Generating docs for compound AssociativeArray...
Generating docs for compound Boolean...
      ...
[ 19%] Building C object 3rdParty/bzip2/CMakeFiles/bzip2.dir/randtable.o
Linking C static library ../../libs/libbzip2.a
[ 19%] Built target bzip2
Scanning dependencies of target unzip
[ 20%] Building C object 3rdParty/unzip/CMakeFiles/unzip.dir/unzip.o
Linking C static library ../../libs/libunzip.a
[ 20%] Built target unzip
Scanning dependencies of target madeline2
[ 22%] Building CXX object src/CMakeFiles/madeline2.dir/Affected.o
[ 23%] Building CXX object src/CMakeFiles/madeline2.dir/Boolean.o
[ 25%] Building CXX object src/CMakeFiles/madeline2.dir/Carrier.o
[ 26%] Building CXX object src/CMakeFiles/madeline2.dir/CLP.o
       ...
[ 98%] Building CXX object src/CMakeFiles/madeline2.dir/XMLTagManager.o
[100%] Building CXX object src/CMakeFiles/madeline2.dir/main.o
Linking CXX executable ../bin/madeline2
[100%] Built target madeline2
~>

Step 4: Install

Run make install as root:

~> su -c "make install"
~> password: ******
      ...
Linking CXX executable CMakeFiles/CMakeRelink.dir/madeline2
Install the project...
-- Install configuration: ""
-- Install configuration: ""
-- Install configuration: ""
-- Install configuration: ""
-- Install configuration: ""
-- Installing /usr/local/share/locale/fr/LC_MESSAGES/madeline2.mo
-- Installing /usr/local/share/locale/th/LC_MESSAGES/madeline2.mo
-- Installing /usr/local/share/locale/zh_CN/LC_MESSAGES/madeline2.mo
-- Installing /usr/local/share/locale/zh_TW/LC_MESSAGES/madeline2.mo
-- Install configuration: ""
-- Installing /usr/local/docs/AUTHORS
-- Install configuration: ""
-- Installing /usr/local/bin/madeline2
~>

That's it! You are done.

Running Madeline

Now try running madeline using one of the online test data sets:

~> madeline2 -L "IndividualId DOB" http://eyegene.ophthy.med.umich.edu/madeline/testdata/input/cs_010.data
ShowColumns is
IndividualId      DOB      Total: 2
Parser::readNetworkFile(): Opening network file http://eyegene.ophthy.med.umich.edu/madeline/testdata/input/cs_010.data ...
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in Madeline flat file format ...
 iconColumns size 1
Table 1 is a pedigree table.
Start of addPedigreesFromDataTable
Siblings are ordered by DOB.
End of addPedigreesFromDataTable
Start of draw
No of labels: 2
Pedigree output file is "cs_010ped.xml"
End of draw
~> inkscape cs_010ped.xml &

The resulting cs_010ped.xml file should look like the following when viewed in inkscape or another SVG viewer:

Troubleshooting

When running make in Ubuntu you see an error message like GETTEXT_MSGFMT_EXECUTABLE-NOTFOUND
Use apt-get to install gettext
```
      apt-get install build-essential gettext
      ./configure --with-include-gettext
    
```

Mac OS X

Introduction

Madeline builds quite easily under OSX using a toolset environment such as Macports.

We highly recommend that you build Madeline from source code in order to get the latest improvements. However, if for some reason you don't want to bother with building Madeline from the source tree, Daniel Johnson has kindly provided a Fink package to install Madeline-2.0 PDE on OS X.

Building Madeline on OS X is very similar to the procedure on Linux. Start by opening up a terminal window. Before proceeding with building Madeline, check that you have the prerequisites shown below installed. In order to reduce problems, notice that I suggest building some prerequisites on the command line from source and installing in /usr/local.

Prerequisites

Apple's XCode development environment is required to build Madeline on OS X. XCode includes Apple's version of the GCC compiler, GNU make, and other required tools.
The Git source code management tool is needed to checkout the latest Madeline source code tree. Assuming that you have Macports installed, you can install git using the following command:

sudo port install git
Password: xxxxxxx
--->  Computing dependencies for git
--->  Activating git @2.5.3_0+credential_osxkeychain+doc+pcre+perl5_16+python27
--->  Cleaning git
--->  Scanning binaries for linking errors

Alternatively, just install git from source code.
CMake is a modern cross-platform build system used by Madeline. Although a graphical version of CMake is available for OS X, I found it necessary to compile and install CMake from source code (be sure to check the web for the latest version!). These instructions will install cmake in /usr/local/:

~> wget http://www.cmake.org/files/v2.6/cmake-2.6.3.tar.gz
~> tar xzf cmake-2.6.3.tar.gz
~> cd cmake-2.6.3
~> ./configure
~> make
~> sudo make install
password: ******
~>

GNU gettext provides a framework for loading multi-lingual message catalogs. I found it was necessary to build gettext from source code on OS X (check for latest version before copying these directions!). These instructions will install gettext in /usr/local:

~> wget wget ftp.gnu.org:/pub/gnu/gettext/gettext-0.17.tar.gz 
~> tar xzf gettext-0.17.tar.gz
~> cd gettext-0.17
~> ./configure
~> make
~> sudo make install
password: ******
~>

OpenSSL, LibCurl, and LibXML2 along with development headers should all be available once XCode is installed.

Inkscape is an Open Source scalable vector graphics (SVG) editor with capabilities similar to Adobe Illustrator, CorelDraw, or Xara X. A version for OS X is available. It requires X Windows which is installed by default on OS X 10.5.x (Leopard) and later. Download and install Inkscape if you don't already have a program for viewing and editing the pedigree drawings produced by Madeline.

OK, we are now ready to build the software. These steps are identical to those on Linux:

Step 1: Get the source

Please see the directions above in the Linux section which describe how to check out Madeline from GitHub.

Step 2: Configure

Please see the directions above in the Linux section which describe how to configure and compile Madeline.

Step 3: Build

~> make
    ...

Step 4: Install

~> sudo make install
password: ******
    ...

That's it!

Running Madeline

Try running madeline using one of the online test data sets. Note the command for running Inkscape from the OS X terminal window:

~> madeline2 -L "IndividualId DOB" http://eyegene.ophthy.med.umich.edu/madeline/testdata/input/cs_010.data
     ...
Pedigree output file is "cs_010ped.xml"
End of draw
~> open -a inkscape cs_010ped.xml

Windows

Introduction

Building Madeline on Windows (XP, Vista) currently requires Cygwin. Once Cygwin along with all dependencies have been properly installed, installing Madeline is very similar to the procedure on Linux.

Prerequisites

Cygwin is a Linux-like environment for Windows. It consists of a number of tools and dynamic link libraries (DLLs) which at the current time are required to build Madeline on modern Windows (XP and Vista) platforms.
After starting the Cygwin installer, choose " Install from Internet ".
Choose " Install For All Users (RECOMMENDED) ".
Choose " Default Text File Type Unix/binary (RECOMMENDED) ".
Normally you can just select " Direct Connection " and choose any download mirror near you.
The Cygwin installer allows you to choose a number of packages. Be sure to select the following items for installation. All of these should be present under the "Devel" tab (although they may also be repeated under other tabs):
- autoconf
- binutils
- cmake
- curl-devel
- doxygen (optional)
- gcc-g++
- gettext-devel
- libxml2-devel
- make
- openssl-devel
- git

Installing Cygwin may take some time. Be patient ...

Inkscape is an Open Source scalable vector graphics (SVG) editor with capabilities similar to Adobe Illustrator, CorelDraw, or Xara X. A version for Windows is available. Download and install Inkscape if you don't already have a program for viewing and editing the pedigree drawings produced by Madeline.

OK, we are now ready to build the software. From this point on, the steps are identical to those on Linux:

Step 1: Get the source

Please see the instructions above in the Linux section which describe how to check out Madeline from GitHub.

Step 2: Configure

Please see the instructions above in the Linux section which describe how to configure Madeline.

Step 3: Build

~> make
    ...

Step 4: Install

On Windows you probably will not need to become admin to do the install:

~> make install
password: ******
    ...

That's it!

Running Madeline

Try running madeline using one of the online test data sets:

~> madeline2 -L "IndividualId DOB" http://eyegene.ophthy.med.umich.edu/madeline/testdata/input/cs_010.data
     ...
Pedigree output file is "cs_010ped.xml"
End of draw
~>

Then try viewing the resulting file, cs_010ped.xml in Inkscape or another vector graphics viewer.

* * * END OF DOCUMENT * * *

Madeline 2.0 PDE Installation Instructions

Linux and Similar Systems

Introduction

Prerequisites

Recommended

Optional

Step 1: Get the source

Step 2: Configure

Step 3: Build

Step 4: Install

Running Madeline

Troubleshooting

Mac OS X

Introduction

Prerequisites

Recommended

Step 1: Get the source

Step 2: Configure

Step 3: Build

Step 4: Install

Running Madeline

Windows

Introduction

Prerequisites

Recommended

Step 1: Get the source

Step 2: Configure

Step 3: Build

Step 4: Install

Running Madeline