Irwin tool enhancements

Various tool enhancements:
- I realized the only difference between DownloadPackage and DownloadScript was that the latter defaults to the build directory, and uses a relative path, both of which make sense for DownloadPackage as well. So, I made these changes to DownloadPackage and got rid of DownloadScript
- Handle bz2 compression in DownloadPackage
- Added post_download_command argument to DownloadPackage, a command that will be executed in the destination directory. Saves us from making a new class just to do a make.
- Created tools for samtools and picard.
Do you think it might be (optionally, if specified) worth checking os.system(self.post_download_command) for a return code and raise an exception on failure?  Of course, it depends on what the command is, which is why the failure condition would have to be optionally specified... dunno if it's too complicated to generalize...