What are Make's advantages (over Perl and shell scripts)?
Make forces you to think about file transformation in terms of inputs and outputs, recipes and rules. In Perl you are forced to think at the level of
variables, conditionals, and loops. In Shell you are forced to think like a caveman.
Unfortunately, bioinformatics is still largely about files and their suffixes. Make has a very powerful syntax based almost entirely around file suffixes.
Make knows what's been made and what hasn't. Make can be interrupted and restarted safely, and without overwriting finished work.
Make knows what's changed and what hasn't. If an input is newer than an output, it will attempt to rebuild the output.
Make allows you to add new input files without worrying about overwriting old ones.
Make is well supported. There are 1333 Make questions on SO alone.
When people see a Makefile, they immediately know how to run it.
Make does not force you to wrap shell statements in quotes.
Make is a DSL. It will attempt to validate your syntax.
Make is ancient, ubiquitous, and reliable.
Make can parallelize with --jobs.
Make recipes encourage reuse.
Addresses Makefile weaknesses without
throwing out the good stuff
Difficult to implement control flow
No cluster support
Too much reliance on sentinal files
No reporting mechanism