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.
Oh wait, I misread this diff, sorry. I thought there were multiple elif clauses (one for tar.gz and one for tar.bz2) with a typo in one of the elif clauses. Now I see that it's a single clause that handles both cases. Nevermind!