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.
Immediately after the call to post_download is a call to verify_install which checks the existence (and usually, executability) of targetpath. So if "make" fails it will get caught immediately even without checking the return code of os.system. Still, it would be good to check the return code for other cases and to give better feedback about what failed.