My short course about "Make"/"Makefile" and bioinformatics. January 2013

1. Make
Pierre Lindenbaum
http://plindenbaum.blogspot.com
@yokofakun(http://twitter.com/yokofakun)
INSERM-UMR1087 Nantes
January 2013
https://github.com/lindenb/courses/tree/master/about.make

2. Problem

3. Build a C program

4. Make a protein
#!/bin/bash
TRANSCRIPT=cat
TRANSLATE=cat
rm -f merge.protein
for DNA in file1.dna file2.dna file3.dna
do
echo "ATGCTAGTAGATGC" > ${DNA}
${TRANSCRIPT} ${DNA} > ${DNA/%.dna/.rna}
${TRANSLATE} ${DNA/%.dna/.rna} > ${DNA/%.dna/.pep}
cat ${DNA/%.dna/.pep} >> merge.protein
done

5. What if file1.pep already exists ?

6. Solution: Test if file exists
#!/bin/bash
TRANSCRIPT=cat
TRANSLATE=cat
rm -f merge.protein
for DNA in file1.dna file2.dna file3.dna
do
echo "ATGCTAGTAGATGC" > ${DNA}
${TRANSCRIPT} ${DNA} > ${DNA/%.dna/.rna}
if [ ! -f ${DNA/%.dna/.pep} ]
then
${TRANSLATE} ${DNA/%.dna/.rna} > ${DNA/%.dna/.pep}
fi
cat ${DNA/%.dna/.pep} >> merge.protein
done

7. What if file1.pep is outdated ?

8. Parallelization ?

9. GNU make

10. "a utility that automatically
builds executable programs and
libraries from source code by
reading files called makefiles"

11. 1977

12. TARGET1: DEPENDENCIES
COMMAND-LINES1
COMMAND-LINES2
COMMAND-LINES3

13. Makefile
TRANSCRIPT=cat
TRANSLATE=cat
merged.protein: file1.pep file2.pep file3.pep
cat file1.pep file2.pep
file3.pep > merged.protein
file1.pep: file1.rna
${TRANSLATE} file1.rna > file1.pep
file1.rna : file1.dna
${TRANSCRIPT} file1.dna > file1.rna
file1.dna:
echo "ATGCTAGTAGATGC" > file1.dna

14. Output
echo "ATGCTAGTAGATGC" > file1.dna
cat file1.dna > file1.rna
cat file1.rna > file1.pep
echo "ATGCTAGTAGATGC" > file2.dna
cat file2.dna > file2.rna
cat file2.rna > file2.pep
echo "ATGCTAGTAGATGC" > file3.dna
cat file3.dna > file3.rna
cat file3.rna > file3.pep
cat file1.pep file2.pep
file3.pep > merged.protein

15. If one file is removed
$ rm file2.rna
$ make
cat file2.dna > file2.rna
cat file2.rna > file2.pep
cat file1.pep file2.pep
file3.pep > merged.protein

16. If one file is changed
$ touch file1.dna file3.pep
$ make
cat file1.dna > file1.rna
cat file1.rna > file1.pep
cat file1.pep file2.pep
file3.pep > merged.protein

17. Special variables

18. "name of the target" : $@
TRANSCRIPT=cat
TRANSLATE=cat
merged.protein: file1.pep file2.pep file3.pep
cat file1.pep file2.pep
file3.pep > $@
file1.pep: file1.rna
${TRANSLATE} file1.rna > $@
file1.rna : file1.dna
${TRANSCRIPT} file1.dna > $@
file1.dna:
echo "ATGCTAGTAGATGC" > $@

19. "name of the first dependency" : $<
TRANSCRIPT=cat
TRANSLATE=cat
merged.protein: file1.pep file2.pep file3.pep
cat file1.pep file2.pep
file3.pep > $@
file1.pep: file1.rna
${TRANSLATE} $< > $@
file1.rna : file1.dna
${TRANSCRIPT} $< > $@
file1.dna:
echo "ATGCTAGTAGATGC" > $@

20. "all the dependencies" : $^
TRANSCRIPT=cat
TRANSLATE=cat
merged.protein: file1.pep file2.pep file3.pep
cat $^ > $@
file1.pep: file1.rna
${TRANSLATE} $< > $@
file1.rna : file1.dna
${TRANSCRIPT} $< > $@
file1.dna:
echo "ATGCTAGTAGATGC" > $@
file2.pep: file2.rna

21. Rules

22. How to create a *.pep or a *.rna ?
TRANSCRIPT=cat
TRANSLATE=cat
%.pep:%.rna
${TRANSLATE} $< > $@
%.rna:%.dna
${TRANSCRIPT} $< > $@
merged.protein: file1.pep file2.pep file3.pep
cat $^ > $@
file1.dna:
echo "ATGCTAGTAGATGC" > $@
file2.dna:
echo "ATGCTAGTAGATGC" > $@
file3.dna:
echo "ATGCTAGTAGATGC" > $@

23. Output
echo "ATGCTAGTAGATGC" > file1.dna
cat file1.dna > file1.rna
cat file1.rna > file1.pep
echo "ATGCTAGTAGATGC" > file2.dna
cat file2.dna > file2.rna
cat file2.rna > file2.pep
echo "ATGCTAGTAGATGC" > file3.dna
cat file3.dna > file3.rna
cat file3.rna > file3.pep
cat file1.pep file2.pep file3.pep > merged.prot

24. Useful options

25. -B "Unconditionally make all targets"

26. -f FILE "Read FILE as a makefile"

27. -j [N] "Allow N jobs at once"

28. -n "Don't actually run any commands; just print them"

29. .PHONY targets
.PHONY: all clean
all: file1.dna
file1.dna:
echo "ATGCTAGTAGATGC" > $@
clean:
rm -f file1.dna

30. Function Call Syntax
$(function arg1,arg2,arg3...)

31. Loops: $(foreach var,list,...)
merged.protein:
$(foreach INDEX,1 2 3,file${INDEX}.pep )
cat $^ > $@

32. $(eval )
TRANSCRIPT=cat
TRANSLATE=cat
INDEXES=1 2 3
%.pep:%.rna
${TRANSLATE} $< > $@
%.rna:%.dna
${TRANSCRIPT} $< > $@
merged.protein: $(foreach INDEX,${INDEXES},file${INDEX}
cat $^ > $@
$(foreach INDEX,${INDEXES},$(eval
file${INDEX}:
echo "ATGCTAGTAGATGC" > $$@
))

33. $(subst ee,EE,feet on the street)
‘fEEt on the strEEt’.
$(patsubst %.c,%.o,x.c.c bar.c)
‘x.c.o bar.o’.
$(strip a b c )
‘a b c’

34. $(filter %.c,src1.c src2.c src3.c file.txt)
$(filter-out %.c,src1.c src2.c src3.c file.txt)
$(sort foo bar lose)
$(word 2, foo bar baz)
'bar'
$(wordlist 2, 3, foo bar baz)
‘bar baz’.
$(firstword foo bar)
‘foo’.
$(lastword foo bar)
‘bar’.

35. $(dir src/foo.c hacks)
‘src/ ./’
$(notdir src/foo.c hacks)
‘foo.c hacks’
$(suffix src/foo.c src-1.0/bar.c hacks)
‘.c .c’
$(basename src/foo.c src-1.0/bar hacks)
‘src/foo src-1.0/bar hacks’
$(addsuffix .c,foo bar)
‘foo.c bar.c’.
$(addprefix src/,foo bar)
‘src/foo src/bar’

36. (join a b,.c .o)
‘a.c b.o’
$(shell cat file1.txt)

37. END