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.
Also, ideally the semicolon should be changed to && but since mkdir_p already checked that the directory is present and is a directory I can't think of a case where it would actually make a difference.