Testing on cygwin

configure

@@ -22,6 +22,12 @@ if [ ! -d ./src ]; then
 	exit 1
 fi
 
+if [ -d .git ]; then
+  echo "Updating git submodules"
+  git submodule init
+  git submodule update
+fi
+
 language=$1
 if [ -z $language ]; then
   language='--with-perl'

doc/TROUBLESHOOTING.txt

@@ -0,0 +1,21 @@
+= Trouble shooting =
+
+Listed below are common errors seen when building BioLib.
+
+See also ./doc/REPORTINGBUGS.txt if you want to send a problem
+upstream.
+
+== Could not find Cmake module =
+
+An error like:
+
+  Could not find module FindGitSubmodule.cmake or a configuration file for package GitSubmodule 
+
+Points out the cmake-support submodule has not been initialized in
+the source repository. BioLib uses submodules to bring together
+different git repositories. Fix with:
+
+  git submodule init
+  git submodule update
+
+(this should be done by the configure script)

doc/WINDOWS.txt

@@ -0,0 +1,23 @@
+= BioLib on Microsoft Windows =
+
+The BioLib build system supports building on Cygwin
+(http://www.cygwin.com/). First install Cygwin on your machine
+selecting the following packages:
+
+* cmake   (development)
+* gcc-g++ (development)
+* make    (development)
+* swig    (development)
+* your preferred language: perl, python and/or ruby
+
+and, optionally:
+
+* git (to fetch the latest repositories)
+
+for ASciLib:
+
+* autoconf (development)
+* automake (development)
+
+NOTE: The AffyIO module does not yet work on Cygwin - there is a
+dependency on the R libraries.