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.
It is probably worthwhile to add such a check. (No need to make it optional; if it is not desired the caller can just override post_download.) I figured that the subsequent check that the executable is present should be good enough, but that won't handle the case that the postprocess modifies a downloaded executable instead of creating a new one.