How to Fix Hadoop for non-Unix platform (Windows OS) ?

Users of org.expasy.jpl.io.util.JPLHMapSerializer on windows may experiment the following exception as Hadoop makes system call to unix tool chmod :

Exception in thread "main" java.io.IOException: Cannot run program "chmod": CreateProcess error=2,
The system cannot find the file specified :
        at java.lang.ProcessBuilder.start(Unknown Source)
        at org.apache.hadoop.util.Shell.runCommand(Shell.java:201)
        at org.apache.hadoop.util.Shell.run(Shell.java:183)
        at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:376)
        at org.apache.hadoop.util.Shell.execCommand(Shell.java:462)
        at org.apache.hadoop.util.Shell.execCommand(Shell.java:445)
        at org.apache.hadoop.fs.RawLocalFileSystem.execCommand(RawLocalFileSystem.java:543)
        at org.apache.hadoop.fs.RawLocalFileSystem.setPermission(RawLocalFileSystem.java:535)
        at org.apache.hadoop.fs.FilterFileSystem.setPermission(FilterFileSystem.java:336)
        at org.apache.hadoop.fs.ChecksumFileSystem.create(ChecksumFileSystem.java:400)
        at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:610)
        at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:591)
        at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:498)
        at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:490)
        at org.apache.hadoop.hbase.io.hfile.HFile$Writer.<init>(HFile.java:306)
        at org.expasy.jpl.io.util.JPLHMapSerializer.init(JPLHMapSerializer.java:125)
     	

The solution is to install cygwin in your windows system or install a subset of it as only chmod and its dlls are needed. We will provide, in the following, a solution for the second alternative:

First Step: Get "chmod" Resources

Here are the archives for different Windows architectures:

• Windows 32-bit - contains chmod.exe, cygwin1.dll, cygiconv-2.dll, cygintl-8.dll and cyggcc_s-1.dll
• Windows 64-bit - not yet available

Second Step: Set your Path in Windows

Do not forget to set your PATH variable for chmod in Windows else chmod will not be found!!

1. First right-click on your My Computer icon on your Desktop and click on Properties. Alternatively you could just press the Windows Key+Pause Break Key
2. Then in the new window that opened, click on the Advanced tab
3. Click on Environment Variables
4. In System Variables, edit or create the PATH variable and enter the path name to cygwin-chmod directory