When batch processing is necessary (no manual intervention, as in a reproducible project), shell scripts are usually the first solution that come to mind. However, the inherent complexity and non-linearity of progress in a scientific project (where experimentation is key) make it hard to manage the script(s) as the project evolves. For example, a script will start from the top/start every time it is run. So if you have already completed 90% of a research project and want to run the remaining 10% that you have newly added, you have to run the whole script from the start again. Only then will you see the effects of the last new steps (to find possible errors, or better solutions and etc).
It is possible to manually ignore/comment parts of a script to only do a special part. However, such checks/comments will only add to the complexity of the script and will discourage you to play-with/change an already completed part of the project when an idea suddenly comes up. It is also prone to very serious bugs in the end (when trying to reproduce from scratch). Such bugs are very hard to notice during the work and frustrating to find in the end.
The Make paradigm, on the other hand, starts from the end: the final target. It builds a dependency tree internally, and finds where it should start each time the project is run. Therefore, in the scenario above, a researcher that has just added the final 10% of steps of her research to her Makefile, will only have to run those extra steps. With Make, it is also trivial to change the processing of any intermediate (already written) rule (or step) in the middle of an already written analysis: the next time Make is run, only rules that are affected by the changes/additions will be re-run, not the whole analysis/project.
This greatly speeds up the processing (enabling creative changes), while keeping all the dependencies clearly documented (as part of the Make language), and most importantly, enabling full reproducibility from scratch with no changes in the project code that was working during the research. This will allow robust results and let the scientists get to what they do best: experiment and be critical to the methods/analysis without having to waste energy and time on technical problems that come up as a result of that experimentation in scripts.
Since the dependencies are clearly demarcated in Make, it can identify independent steps and run them in parallel. This further speeds up the processing. Make was designed for this purpose. It is how huge projects like all Unix-like operating systems (including GNU/Linux or Mac OS operating systems) and their core components are built. Therefore, Make is a highly mature paradigm/system with robust and highly efficient implementations in various operating systems perfectly suited for a complex non-linear research project.
Make is a small language with the aim of defining rules containing targets, prerequisites and recipes. It comes with some nice features like functions or automatic-variables to greatly facilitate the management of text (filenames for example) or any of those constructs. For a more detailed (yet still general) introduction see the article on Wikipedia:
Make is a +40 year old software that is still evolving, therefore many implementations of Make exist. The only difference in them is some extra features over the standard definition (which is shared in all of them). Maneage is primarily written in GNU Make (which it installs itself, you don't have to have it on your system). GNU Make is the most common, most actively developed, and most advanced implementation. Just note that Maneage downloads, builds, internally installs, and uses its own dependencies (including GNU Make), so you don't have to have it installed before you try it out.
The GNU Make book/manual (links below) is arguably the best place to learn Make. It is an excellent and non-technical book to help get started (it is only non-technical in its first few chapters to get you started easily). It is freely available and always up to date with the current GNU Make release. It also clearly explains which features are specific to GNU Make and which are general in all implementations. So the first few chapters regarding the generalities are useful for all implementations.
The first link below points to the GNU Make manual in various formats and in the second, you can download it in PDF (which may be easier for a first time reading).
If you use GNU Make, you also have the whole GNU Make manual on the
command-line with the following command (you can come out of the "Info"
environment by pressing
If you aren't familiar with the Info documentation format, we strongly
$ info info and reading along. In less than an hour,
you will become highly proficient in it (it is very simple and has a great
manual for itself). Info greatly simplifies your access (without taking
your hands off the keyboard!) to many manuals that are installed on your
system, allowing you to be much more efficient as you work. If you use the
GNU Emacs text editor (or any of its variants), you also have access to all
Info manuals while you are writing your projects (again, without taking
your hands off the keyboard!).