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.
I was just adding the .tar.bz2 case to the previously handled options .tar.gz and .tgz. We can also add .tbz as a 4th case; it would also need to be added to the subsequent line defining compression_option. (I've never actually encountered a tbz file, so I don't know if it is needed, but it wouldn't hurt.)