This is a make-like utility for managing builds (or analysis workflows) involving multiple dependent files. It supports most of the functionality of GNU Make, along with neat extensions like cluster-based job processing, multiple wildcards per target, MD5 checksums instead of timestamps, and declarative logic programming in Prolog.

Indeed: Prolog. No knowledge of the dark logical arts is necessary to use Biomake; the software can be run directly off a GNU Makefile. However, if you know (or are prepared to learn) a little Prolog, you can do a lot more. And, really, logic programming is the way you should be specifying workflow dependencies and build chains; so what are you waiting for?

1. Install SWI-Prolog from http://www.swi-prolog.org

2. Get the latest biomake source from github. No installation steps are required. Just add it to your path (changing the directory if necessary):

   export PATH=$PATH:$HOME/biomake/bin

3. Get (minimal) help from the command line:

   biomake -h

4. Create a 'Makefile' or a 'Makeprog' (see below)

If you want to install biomake in /usr/local/bin instead of adding it to your path, type make install in the top level directory of the repository. (This just creates a symlink, so be sure to put the repository somewhere safe beforehand, and don't remove it after installation.)

You can also try make test to run the test suite.

The program can also be installed via the SWI-Prolog pack system. Just start SWI and type:

?- pack_install('biomake').

biomake [OPTIONS] [TARGETS]

-h,--help 
    Show help
-v,--version 
    Show version
-n,--dry-run,--recon,--just-print 
    Print the commands that would be executed, but do not execute them
-B,--always-make 
    Always build fresh target even if dependency is up to date
-f,--file,--makefile GNUMAKEFILE
    Use a GNU Makefile as the build specification [default: Makefile]
-p,--prog,--makeprog MAKEPROG
    Use MAKEPROG as the (Prolog) build specification [default: Makeprog]
-m,--eval,--makefile-syntax STRING
    Evaluate STRING as GNU Makefile syntax
-P,--eval-prolog,--makeprog-syntax STRING
    Evaluate STRING as Prolog Makeprog syntax
-I,--include-dir DIR
    Specify search directory for included Makefiles
--target TARGET
    Force biomake to recognize a target even if it looks like an option
-T,--translate,--save-prolog FILE
    Translate GNU Makefile to Prolog Makeprog syntax
-W,--what-if,--new-file,--assume-new TARGET
    Pretend that TARGET has been modified
-o,--old-file,--assume-old TARGET
    Do not remake TARGET, or remake anything on account of it
-k,--keep-going 
    Keep going after error
-S,--no-keep-going,--stop 
    Stop after error
-t,--touch 
    Touch files (and update MD5 hashes, if appropriate) instead of running recipes
-D,--define Var Val
    Assign Makefile variables from command line
Var=Val 
    Alternative syntax for '-D Var Val'
-l DIRECTORY
    Iterates through directory writing metadata on each file found
-s,--quiet,--silent 
    Silent operation; do not print recipes as they are executed
--one-shell 
    Run recipes in single shell (equivalent to GNU Make's .ONESHELL)
-H,--md5-hash 
    Use MD5 hashes instead of timestamps
-Q,--queue-engine ENGINE
    Queue recipes using ENGINE (supported: test,sge,pbs,slurm,poolq)
-j,--jobs JOBS
    Number of job threads (poolq engine)
--qsub-exec PATH
    Path to qsub (sge,pbs) or sbatch (slurm)
--qdel-exec PATH
    Path to qdel (sge,pbs) or scancel (slurm)
--queue-args "ARGS"
    Queue-specifying arguments for qsub/qdel (sge,pbs) or sbatch/scancel (slurm)
--qsub-args "ARGS"
    Additional arguments for qsub (sge,pbs) or sbatch (slurm)
--qdel-args "ARGS"
    Additional arguments for qdel (sge,pbs) or scancel (slurm)
--flush,--qsub-flush <target or directory>
    Erase all jobs for given target/dir
--debug MSG
    [developers] Debugging messages. MSG can be build, pattern, makefile, md5...
--trace predicate
    [developers] Print debugging trace for given predicate
--no-backtrace 
    [developers] Do not print a backtrace on error

Brief overview:

• Prolog can be embedded within prolog and endprolog directives
• $(bagof Template,Goal) expands to the space-separated List from the Prolog bagof(Template,Goal,List)
• Following the dependent list with {Goal} causes the rule to match only if Goal is satisfied. The special variables TARGET and DEPS, if used, will be bound to the target and dependency-list (i.e. $@ and $^, loosely speaking; except the latter is a true Prolog list, not encoded as a string with whitespace separators as in GNU Make)

This assumes some knowledge of GNU Make and Makefiles.

Unlike makefiles, biomake allows multiple variables in pattern matching. Let's say we have a program called align that compares two files producing some output (e.g. biological sequence alignment, or ontology alignment). Assume our file convention is to suffix ".fa" on the inputs. We can write a Makefile with the following:

align-$X-$Y: $X.fa $Y.fa
    align $X.fa $Y.fa > $@

Now if we have files x.fa and y.fa we can type:

biomake align-x-y

Prolog extensions allow us to do even fancier things with logic. Specifically, we can embed arbitrary Prolog, including both database facts and rules. We can use these rules to control flow in a way that is more powerful than makefiles.

Let's say we only want to run a certain program when the inputs match a certain table in our database. We can embed Prolog in our Makefile as follows:

prolog
sp(mouse).
sp(human).
sp(zebrafish).
endprolog

align-$X-$Y: $X.fa $Y.fa {sp(X),sp(Y)}
    align $X.fa $Y.fa > $@

The lines beginning sp between prolog and endprolog define the set of species that we want the rule to apply to. The rule itself consists of 4 parts:

• the target (align-$X-$Y)
• the dependencies ($X.fa and $Y.fa)
• a Prolog goal, enclosed in braces ({sp(X),sp(Y)}), that is used as an additional logic test of whether the rule can be applied
• the command (align ...)

In this case, the Prolog goal succeeds with 9 solutions, with 3 different values for X and Y. If we type...

biomake align-platypus-coelacanth

...it will not succeed, even if the .fa files are on the filesystem. This is because the goal {sp(X),sp(Y)} cannot be satisfied for these two values of X and Y.

To get a list of all matching targets, we can use the special BioMake function $(bagof...) which wraps the Prolog predicate bagof/3. The following example also uses the Prolog predicates format/2 and format/3, for formatted output:

prolog

sp(mouse).
sp(human).
sp(zebrafish).

ordered_pair(X,Y) :- sp(X),sp(Y),X@<Y.

make_filename(F) :-
  ordered_pair(X,Y),
  format(atom(F),"align-~w-~w",[X,Y]).

endprolog

all: $(bagof F,make_filename(F))

align-$X-$Y: $X.fa $Y.fa { ordered_pair(X,Y),
                           format("Matched ~w <-- ~n",[TARGET,DEPS]) },
    align $X.fa $Y.fa > $@

Now if we type...

biomake all

...then all non-identical ordered pairs will be compared (since we have required them to be ordered pairs, we get e.g. "mouse-zebrafish" but not "zebrafish-mouse"; the motivation here is that the align program is symmetric, and so only needs to be run once per pair).

If you are a Prolog wizard who finds embedding Prolog in Makefiles too cumbersome, you can use a native Prolog-like syntax. Biomake looks for a Prolog file called Makeprog (or Makespec.pro) in your current directory. (If it's not there, it will try looking for a Makefile in GNU Make format. The following examples describe the Prolog syntax.)

Assume you have two file formats, ".foo" and ".bar", and a foo2bar converter.

Add the following rule to your Makeprog:

'%.bar' <-- '%.foo',
    'foo2bar $< > $@'.

Unlike makefiles, whitespace is irrelevant. However, you do need the quotes, and remember the closing ".", as this is Prolog syntax.

If you prefer to stick with GNU Make syntax, the above Makeprog is equivalent to the following Makefile:

%.bar: %.foo
	   foo2bar $< > $@

To convert a pre-existing file "x.foo" to "x.bar" type:

biomake x.bar

Let's say we can go from a .bar to a .baz using a bar2baz converter. We can add an additional rule:

'%.baz' <-- '%.bar',
    'bar2baz $< > $@'.

Now if we type...

touch x.foo
biomake x.baz

...we get the following output, showing the tree structure of the dependencies:

Checking dependencies: test.baz <-- [test.bar]
    Checking dependencies: test.bar <-- [test.foo]
        Nothing to be done for test.foo
    Target test.bar not materialized - will rebuild if required
    foo2bar x.foo > x.bar
    test.bar is up to date
Target test.baz not materialized - will rebuild if required
bar2baz x.bar > x.baz
test.baz is up to date

The syntax in the makeprog above is designed to be similar to what is already used in makefiles. You can bypass this and use Prolog variables. The following form is functionally equivalent:

'$(Base).bar' <-- '$(Base).foo',
    'foo2bar $(Base).foo > $(Base).bar'.

The equivalent Makefile would be this...

$(Base).bar: $(Base).foo
	foo2bar $(Base).foo > $(Base).bar

...although strictly speaking, this is only equivalent if you are using Biomake; GNU Make's treatment of this Makefile isn't quite equivalent, since unbound variables don't work the same way in GNU Make as they do in Biomake (Biomake will try to use them as wildcards for pattern-matching, whereas GNU Make will just replace them with the empty string - which is also the default behavior for Biomake if they occur outside of a pattern-matching context).

Following the GNU Make convention, variable names must be enclosed in parentheses unless they are single letters.

You can parse a GNU Makefile (including Biomake-specific extensions, if any) and save the corresponding Prolog syntax using the -T option (long-form --translate).

Here is the translation of the Makefile from the previous section (lightly formatted for clarity):

sp(mouse).
sp(human).
sp(zebrafish).

ordered_pair(X,Y):-
 sp(X),
 sp(Y),
 X@<Y.

make_filename(F):-
 ordered_pair(X,Y),
 format(atom(F),"align-~w-~w",[X,Y]).

"all" <-- "$(bagof F,make_filename(F))".

"align-$X-$Y" <--
 ["$X.fa","$Y.fa"],
 {ordered_pair(X,Y),
  format("Matched ~w <-- ~n",[TARGET,DEPS])},
 "align $X.fa $Y.fa > $@".

Note how the list of dependencies in the second rule, which contains more than one dependency ($X.fa and $Y.fa), is enclosed in square brackets, i.e. a Prolog list (["$X.fa","$Y.fa"]). The same syntax applies to rules which have lists of multiple targets, or multiple executables.

The rule for target all in this translation involves a call to the Biomake function $(bagof ...), but (as noted) this function is just a wrapper for the Prolog bagof/3 predicate. The automatic translation is not smart enough to remove this layer of wrapping, but we can do so manually, yielding a clearer program:

sp(mouse).
sp(human).
sp(zebrafish).

ordered_pair(X,Y):-
 sp(X),
 sp(Y),
 X@<Y.

make_filename(F):-
 ordered_pair(X,Y),
 format(atom(F),"align-~w-~w",[X,Y]).

"all" <-- DepList, {bagof(F,make_filename(F),DepList)}.

"align-$X-$Y" <--
 ["$X.fa","$Y.fa"],
 {ordered_pair(X,Y),
  format("Matched ~w <-- ~n",[TARGET,DEPS])},
 "align $X.fa $Y.fa > $@".

Biomake supports most of the functionality of GNU Make, including

• different flavors of variable (recursive, expanded, etc.)
• various ways of setting variables
• appending to variables
• multi-line variables
• automatic variables such as $<, $@, $^, $(@F), etc.
• substitution references
• computed variable names
• all the text functions
• all the filename functions
• the shell function
• user-defined functions
• errors and warnings
• many of the same command-line options
• conditional syntax and conditional functions
• the include directive
• various other quirks of GNU Make syntax e.g. single-line recipes, forced rebuilds

There are slight differences in the way variables are expanded, which arise from the fact that Biomake treats variable expansion as a post-processing step (part of the language) rather than a pre-processing step (which is how GNU Make does it). In Biomake, variable expansions must be aligned with the overall syntactic structure; they cannot span multiple syntactic elements.

As a concrete example, GNU Make allows this sort of thing:

RULE = target: dep1 dep2
$(RULE) dep3

which (in GNU Make, but not biomake) expands to

target: dep1 dep2 dep3

That is, the expansion of the RULE variable spans both the target list and the start of the dependency list. To emulate this behavior faithfully, Biomake would have to do the variable expansion in a separate preprocessing pass - which would mean we couldn't translate variables directly into Prolog. We think it's worth sacrificing this edge case in order to maintain the semantic parallel between Makefile variables and Prolog variables, which allows for some powerful constructs.

The implementation of conditional syntax (ifeq, ifdef and the like) must also be aligned with the syntax: you can only place a conditional at a point where a variable assignment, recipe, or include directive could go (i.e. at the top level of the Makefile grammar).

Unlike GNU Make, Biomake does not offer domain-specific language extensions in Scheme (even though this is one of the cooler aspects of GNU Make), but you can program it in Prolog instead - it's quite hackable.

Biomake provides a few extra functions for arithmetic on lists:

• $(iota N) returns a space-separated list of numbers from 1 to N
• $(iota S,E) returns a space-separated list of numbers from S to E
• $(add X,L) adds X to every element of the space-separated list L
• $(multiply Y,L) multiplies every element of the space-separated list L by Y
• $(divide Z,L) divides every element of the space-separated list L by Z

Instead of using file timestamps, which are fragile (especially on networked filesystems), Biomake can optionally use MD5 checksums to decide when to rebuild files. Turn on this behavior with the -H option (long form --md5-hash).

Biomake uses the external program md5 to do checksums (available on OS X), or md5sum (available on Linux). If neither of these are found, Biomake falls back to using the SWI-Prolog md5 implementation; this does however require loading the entire file into memory (which may be prohibitive for large files).

To run jobs in parallel, locally or on a cluster, you need to specify a queueing engine using the -Q option (long form --queue-engine). Note that, unlike with GNU Make, multi-threading is not activated simply by specifying the number of threads with -j; you need -Q as well.

There are several queueing engines currently supported:

• -Q poolq uses an internal thread pool for running jobs in parallel on the same machine that biomake is running on
• -Q sge uses Sun Grid Engine
• -Q pbs uses PBS
• -Q slurm uses SLURM

For Sun Grid Engine, PBS and SLURM, the paths to the relevant job control executables, and any arguments to those executables (such as the name of the queue that jobs should be run on), can be controlled using various command-line arguments.

Ideas for future development:

• a web-based build environment (a la Galaxy)
• semantic web enhancement (using NEPOMUK file ontology)
• using other back ends and target sources (sqlite db, REST services)
• cloud-based computing
• metadata