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Make makefiles

Make makefiles. pipelining for the masses. Make is based on set of rules. # this is a remark target : prerequisites ... recipe_line1 recipe_line2 . <Tab>. Simple example. Recipe will be executed if either: 1. Target does not exist 2. Target is older than prerequisite.

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Make makefiles

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  1. Make makefiles pipelining for the masses

  2. Make is based on set of rules # this is a remark target : prerequisites ... recipe_line1 recipe_line2 ... <Tab>

  3. Simple example Recipe will be executed if either:1. Target does not exist2. Target is olderthan prerequisite Leg.pdf : Leg.tree R < plotTree.RLeg.tree Leg.tree: Leg.alnRAxML -f a -m GTRGAMMA -s Leg.aln> Leg.tree Leg.aln : Lpne.alnLdra.alnLisr.alnLjor.alnperlfastaMsaConcat.plLpn.alnLdra.aln… > Leg.aln Lpne.aln : Lpne.fasta prank -F Lpne.fasta > Lpne.aln Ldra.aln : Ldra.fastaprank -F Ldra.fasta> Ldra.aln Lisr.aln : Lisr.fasta prank -F Lisr.fasta> Lisr.aln Lsha.aln : Lsha.fasta prank -F Lsha.fasta> Lsha.aln

  4. Makefile is a tree Recipe will be executed if either:1. Target does not exist2. Target is olderthan prerequisite

  5. Simple example Makefile makes the first target (the order of the rest is not important Leg.pdf : Leg.tree R < plotTree.RLeg.tree Leg.tree: Leg.alnRAxML -f a -m GTRGAMMA -s Leg.aln> Leg.tree Leg.aln : Lpne.alnLdra.alnLisr.alnLjor.alnperlfastaMsaConcat.plLpn.alnLdra.aln… > Leg.aln Lpne.aln : Lpne.fasta prank -F Lpne.fasta > Lpne.aln Ldra.aln : Ldra.fastaprank -F Ldra.fasta> Ldra.aln Lisr.aln : Lisr.fasta prank -F Lisr.fasta> Lisr.aln Lsha.aln : Lsha.fasta prank -F Lsha.fasta> Lsha.aln

  6. Variables alns= Lpne.alnLdra.alnLisr.alnLjor.aln Leg.tree.pdf : Leg.tree R < plotTree.RLeg.tree Leg.tree: Leg.alnRAxML -f a -m GTRGAMMA -s Leg.aln> Leg.tree Leg.aln : $(alns)perlfastaMsaConcat.pl$(alns) > Leg.aln Lpne.aln : Lpne.fasta prank -F Lpne.fasta > Lpne.aln Ldra.aln : Ldra.fastaprank -F Ldra.fasta> Ldra.aln Lisr.aln : Lisr.fasta prank -F Lisr.fasta> Lisr.aln Lsha.aln : Lsha.fasta prank -F Lsha.fasta> Lsha.aln

  7. Variables dir= ~/Legionella/Genomes/phase1/ alns= $(dir)Lpne.aln$(dir)Ldra.aln$(dir)Lisr.aln … $(dir)Leg.tree.pdf : $(dir)Leg.tree R < plotTree.R$(dir)Leg.tree $(dir)Leg.tree: $(dir)Leg.alnRAxML -f a -s $(dir)Leg.aln> $(dir)Leg.tree $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$(alns) > $(dir)Leg.aln $(dir)Lpne.aln : $(dir)Lpne.fasta prank -F $(dir)Lpne.fasta > $(dir)Lpne.aln $(dir)Ldra.aln : $(dir)Ldra.fastaprank -F $(dir)Ldra.fasta> $(dir)Ldra.aln $(dir)Lisr.aln : $(dir)Lisr.fasta prank -F $(dir)Lisr.fasta> $(dir)Lisr.aln $(dir)Lsha.aln : $(dir)Lsha.fasta prank -F $(dir)Lsha.fasta> $(dir)Lsha.aln

  8. Special Variables dir= ~/Legionella/Genomes/phase1/ alns = $(dir)Lpne.aln$(dir)Ldra.aln$(dir)Lisr.aln … $(dir)Leg.tree.pdf : $(dir)Leg.tree R < plotTree.R$^ $(dir)Leg.tree: $(dir)Leg.alnRAxML -f a -s $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ $(dir)Lpne.aln : $(dir)Lpne.fasta prank -F $^ > $@ $(dir)Ldra.aln : $(dir)Ldra.fastaprank -F $^ > $@ $(dir)Lisr.aln : $(dir)Lisr.fasta prank -F $^ > $@ $(dir)Lsha.aln : $(dir)Lsha.fasta prank -F $^ > $@ Useful special variables: $@ - the target $^ - all prerequisites $< - first prerequisite

  9. Rulez dir= ~/Legionella/Genomes/phase1/ alns = $(dir)Lpne.aln$(dir)Ldra.aln$(dir)Lisr.aln … $(dir)Leg.tree.pdf : $(dir)Leg.tree R < plotTree.R$^ $(dir)Leg.tree: $(dir)Leg.alnRAxML -f a -s $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta prank -F $^ > $@ Rules will simplify your makefile and raise level of abstraction Another useful special variable is $* that matches %

  10. Rulez dir= ~/Legionella/Genomes/phase1/ alns = $(dir)Lpne.aln$(dir)Ldra.aln$(dir)Lisr.aln … %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.alnRAxML -f a -s $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta prank -F $^ > $@ Intermediate files, which are created by rules and are not specified as targets themselves, are by default deleted after no longer needed. (in a few slides we'll see how to change that behavior) General rules can be transferred among makefiles

  11. Some more variables dir= ~/Legionella/Genomes/phase1/ alns = $(dir)Lpne.aln$(dir)Ldra.aln$(dir)Lisr.aln … ALIGN = prank -F RECONSTRUCT = RAxML-f a -s %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.aln $(RECONSTRUCT) $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta $(ALIGN) $^ > $@ Use variables for things you think you might want to change between runs (e.g., BLAST flags)

  12. Some functions (there are many many more…) $(addsuffix<SUFF>,<LIST>) $(addsuffix .ext,adir/b) => a.extdir/b.ext $(addprefix <PREF>,<LIST>) $(addprefixdir/,a b.ext) => dir/a dir/b.ext $(dir<LIST>) $(dirtmp/a dir/b.ext c) => temp/ dir/ ./ $(notdir<LIST>) $(notdirdir/b.ext c) => b.ext c $(basename<LIST>) $(notdira.Rdir/b.extc) => a dir/b c $(shell <command>)

  13. Function usage dir= ~/Legionella/Genomes/phase1/ alns = $(addprefix $(dir), Lpne.alnLdra.alnLisr.aln …) ALIGN = prank -F RECONSTRUCT = RAxML-f a -s %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.aln $(RECONSTRUCT) $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta $(ALIGN) $^ > $@

  14. Function usage dir= ~/Legionella/Genomes/phase1/ alns= $(addprefix $(dir),$(addsuffix.aln, LpneLdraLisr …)) ALIGN = prank -F RECONSTRUCT = RAxML-f a -s %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.aln $(RECONSTRUCT) $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta $(ALIGN) $^ > $@

  15. More functions $(shell <command>) Executes shell command and returns values as list (newlines are turned to spaces). $(shell cat b.ext) => the content of b.ext (as a list) $(LIST:.fas=.aln) Changes all extensions of LIST Legs = Lpne.fasLdra.fasLisr.fasLjor.fas $(Legs:.aln=.fas) => Lpne.alnLdra.alnLisr.alnLjor.aln

  16. Function usage dir= ~/Legionella/Genomes/phase1/ alns= $($(shell ls $(dir)*.fasta):.fasta=.aln) ALIGN= prank -F RECONSTRUCT = RAxML-f a -s %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.aln $(RECONSTRUCT) $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta $(ALIGN) $^ > $@

  17. Special targets dir= ~/Legionella/Genomes/phase1/ alns= $($(shell ls $(dir)*.fasta):.fasta=.aln) ALIGN = prank -F RECONSTRUCT = RAxML-f a -s All : $(dir)Leg.tree.pdf %.tree.pdf : %.tree R < plotTree.R$^ %.tree : %.aln $(RECONSTRUCT) $^> $@ $(dir)Leg.aln : $(alns)perlfastaMsaConcat.pl$^ > $@ %.aln : %.fasta $(ALIGN) $^ > $@ clean: rm -vf$(dir)Leg.tree.pdf $(dir)Leg.tree$(dir)*.aln .SECONDARY: <targets>Intermediate targets not to removed (no target will save all) .Phony : <targets>A phony target is one that is not really the name of a file. It is just a name for some commands to be executed when you make an explicit request

  18. Invoking makefile By default run make to execute the first target of the file called makefile > make You can invoke a specific target in a specific file: > make -f <makefilename> <TARGET> make -f makeTree.mk clean You can also pass values of variables (will override variables with in the makefile > make -f <makefile name> <VAR>=<value> make -f makeTree.mk DIR=/mydir/

  19. Useful flags for make file -j <n>: use n threads (without n - as many as possible) as makefile knows the dependencies he can run the non-dependent recipes in parallel… -n : just echo commands, do not excute -d : debug (shows you what makefile thinks)

  20. Let's check out some Real-life examples

  21. Here are some makefiles I did • A real makefile example:http://www.tau.ac.il/~davidbur/makePhylogeny.mk • Huge (but well documented) makefile:http://www.tau.ac.il/~davidbur/makeCompileFeaturesByPtts.makefile • I use such a makefile to run the one in (2):http://www.tau.ac.il/~davidbur/makefile • This makefile creates a makefile similar to (3) and executes it (getting weird, isn't it…):http://www.tau.ac.il/~davidbur/makeLearningHappen.makefile

  22. useful tips and hints • -before the commnad will tell make to continue even if the execution of that line fails • When using "$", for example in a Perl oneliner, use $$ to let makefile know you mean the character '$' • Beware of extra spaces at the end of lines • You can use the program/script itself as part of prerequisit • Some time it is useful to invoke make from within a makefile • You can use include FILE to add the content of FILE to this point in the makefile

  23. References GNU make tutorial, everything you want to know about make: http://www.gnu.org/software/make/manual/make.html Eyali's Blog in the post (my initial inspiration): http://lifeofadataminer.blogspot.co.il/2009/08/writing-makefile-instead-of-pipeline.html A pipeline is a make (I think his initial inspiration): http://archive.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefilehttp://archive.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile

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