I have found a very easy way to keep logfiles of the commands that you executed in your shell to generate a certain annotation file for genome. It was inspired by a post on kuro5hin some time ago, Of course, makefiles are better than logfiles, but often you're just hacking around and don't want to bother with escaping those $s and tab-characters.
The people at UCSC keep their logfiles in an editor: "We write our shell commands in the makeDb/*.txt files first, then cut and paste those commands to the command line. If they are incorrect, they are corrected in the *.txt file, then cut and paste again to the command line until they work right. The *.txt file is open in an editor until a sequence of operations is completed. --Hiram"
I prefer my way as it saves me the copy-pasting. The following script allows you to write the last command to a logfile and later run selected commands from your log.
Add these two lines to your .bashrc:
export HISTIGNORE="logadd:log" alias logadd="history -p \!\! >> log.txt" alias log="vim log.txt"
When you type logadd now, the last command you typed will be appended to a file called "log.txt". So its a good habit to use logadd after you have found just the right combination of blat, pslSelect, overlapSelect and faPolyASizes, to be able to track down those nasty mistakes 6 months later.