Windows users will need to visit the appropriate web sites and download and install the relevant binaries for all the dependencies.
To configure the tools, you will need to edit or create several environment variables on your system. Access them by clicking the “Environment Variables” button from Control Panel, System, Advanced tab. Use semicolons to separate multiple directories in the PATH variable.
Download Maven.
Unpack the Maven archive into your Program Files, then add the folder’s bin subdirectory to your PATH environment variable; e.g.:
C:\Program Files\apache-maven-3.0.4\bin
Once set, new Command Prompts will recognize “mvn” as a valid command.
Download and run the CMake installer.
During installation, select the “Add CMake to the system PATH for all users” option to ensure that Bio-Formats build system can find your CMake executable.
Once installed, new Command Prompts will recognize “cmake” and “cmake-gui” as valid commands.
Download Boost.
You can either build and install from source using the instructions in the Boost documentation, or follow the link under ‘Other downloads’ to the prebuilt binaries for several Visual Studio versions.
Download and install the JDK.
After the installation is complete, create a new environment variable called JAVA_HOME pointing to your Java installation; e.g.:
C:\Program Files\Java\jdk1.6.0_25
Setting JAVA_HOME is the easiest way to ensure that Maven can locate Java.
You will also need to append your JDK’s client or server VM folder to the PATH; e.g.:
%JAVA_HOME%\jre\bin\client
This step ensures that a directory containing jvm.dll is present in the PATH. If you do not perform this step, you will receive a runtime error when attempting to initialize a JVM from native code.
Optionally, you can add the bin subdirectory to the PATH; e.g.:
%JAVA_HOME%\bin
Once set, new Command Prompts will recognize (e.g.) “javac” as a valid command.
In addition to the other prerequisites, you will also need a working copy of Visual C++. We have tested compilation with Visual C++ 2005 Professional and Visual C++ 2008 Express; other versions may or may not work.
You can download Visual C++ Express for free.
You must launch the environment at least once before you will be able to compile the Bio-Formats C++ bindings.
Run Command Prompt and change to your Bio-Formats working copy. Then run:
# generate the Bio-Formats C++ bindings
cd components\formats-bsd
mvn -DskipTests package dependency:copy-dependencies cppwrap:wrap
# build the Bio-Formats C++ bindings
cd target\cppwrap
mkdir build
cd build
cmake-gui ..
The CMake GUI will open. Click the Configure button, and a dialog will appear. Select your installed version of Visual Studio, and click Finish.
When configuring, you can use the J2L_WIN_BUILD_DEBUG flag to indicate if this will be a Debug or Release build. If the flag is checked it will build as Debug, unchecked will build as Release.
Once configuration is complete, click Configure again, repeating as necessary until the Generate button becomes available. Then click Generate. Once generation is complete, close the CMake window.
Back at the Command Prompt, type:
start jace.sln
The solution will then open in Visual Studio. Select Release or Debug as appropriate from the drop-down menu. Press F7 to compile (or select Build Solution from the Build menu).