Why I Use Makefile for Processes

  1. Automatically check if target files or source files exist. If the source files are not found, exit the make process. If the target files are found, skip this make step.

  2. Automatically check for changes in target files or source files. If the source files are modified, regenerate the corresponding target files.

  3. Easy to run multiple tasks in parallel using multi-processing.

     make –j $processNumber

  4. Can express complex data flows.

  • Multiple independent parallel running processes data flow.

  • Multiple data flows converge into one.

  • One process splits into multiple data flows.

  • Complex mesh data flow.

  • Can be used for one-click software deployment, such as installing Perl/Python/R packages or other command-line software.

     OBJECTS = $(INSTALL_DIR)/lib/perl5/SVG \
           $(INSTALL_DIR)/lib/perl5/x86_64-linux-gnu-thread-multi/GD.pm \
           $(INSTALL_DIR)/lib/perl5/Parallel/ForkManager.pm \
           $(INSTALL_DIR)/lib/perl5/Carp.pm \
           $(INSTALL_DIR)/lib/perl5/Text/Balanced.pm \
           $(INSTALL_DIR)/lib/perl5/Pod/Usage.pm \
           $(INSTALL_DIR)/lib/perl5/x86_64-linux-thread-multi/Params/Validate.pm \
           $(INSTALL_DIR)/lib/perl5/Font/TTF.pm \
           $(INSTALL_DIR)/lib/perl5/x86_64-linux-thread-multi/Clone.pm \
           $(INSTALL_DIR)/lib/perl5/Math/Round.pm \
           $(INSTALL_DIR)/lib/perl5/Statistics/Basic.pm \
           $(INSTALL_DIR)/lib/perl5/Readonly.pm \
           $(INSTALL_DIR)/lib/perl5/x86_64-linux-thread-multi/Storable.pm \
           $(INSTALL_DIR)/lib/perl5/Config/General.pm \
           $(INSTALL_DIR)/lib/perl5/Math/BigInt.pm \
           $(INSTALL_DIR)/lib/perl5/Text/Format.pm \
           $(INSTALL_DIR)/lib/perl5/x86_64-linux-thread-multi/Time/HiRes.pm \
           $(INSTALL_DIR)/lib/perl5/Set/IntSpan.pm \
           $(INSTALL_DIR)/lib/perl5/Regexp/Common.pm \
           $(INSTALL_DIR)/lib/perl5/Memoize.pm \
           $(INSTALL_DIR)/lib/perl5/Math/VecStat.pm \
           $(INSTALL_DIR)/lib/perl5/Math/Bezier.pm

 .PHONY: all
 INSTALL_DIR = $(CURDIR)/../PERL5LIB
 all:program
     $(shell export PERL5LIB=$(PERL5LIB):$(INSTALL_DIR)/lib/perl5)
 program: $(OBJECTS)

 define InstallPerlPM
 $(INSTALL_DIR)/lib/perl5/$1 : $2
     test -d $(INSTALL_DIR) || mkdir -p $(INSTALL_DIR);\
     tar -zxvf $3.tar.gz;\
     cd $3;\
     perl Makefile.PL INSTALL_BASE=$(INSTALL_DIR);\
     make;\
     make install;\
     cd $(CURDIR) && rm -rf $3
 endef

 define InstallPerlPM2
 $(INSTALL_DIR)/lib/perl5/$1 : $2
     test -d $(INSTALL_DIR) || mkdir -p $(INSTALL_DIR);\
     tar -zxvf $3.tgz;\
     cd $3;\
     perl Makefile.PL INSTALL_BASE=$(INSTALL_DIR);\
     make;\
     make install;\
     cd $(CURDIR) && rm -rf $3
 endef

 define InstallPerlPM3
 $(INSTALL_DIR)/lib/perl5/$1 : $2
     test -d $(INSTALL_DIR) || mkdir -p $(INSTALL_DIR);\
     tar -zxvf $3.tar.gz;\
     cd $3;\
     perl Build.PL --install_base $(INSTALL_DIR);\
     ./Build;\
     ./Build test;\
     ./Build install --install_base $(INSTALL_DIR);\
     cd $(CURDIR) && rm -rf $3
 endef

 $(eval $(call InstallPerlPM,Font/TTF.pm,Font-TTF-1.05.tar.gz,Font-TTF-1.05))
 $(eval $(call InstallPerlPM,x86_64-linux-gnu-thread-multi/GD.pm,GD-2.53.tar.gz,GD-2.53))
 $(eval $(call InstallPerlPM,SVG,SVG-2.63.tar.gz,SVG-2.63))
 $(eval $(call InstallPerlPM,Test/Fatal.pm,Test-Fatal-0.014.tar.gz,Test-Fatal-0.014))
 $(eval $(call InstallPerlPM,Test/Requires.pm,Test-Requires-0.08.tar.gz,Test-Requires-0.08))
 $(eval $(call InstallPerlPM,Module/Runtime.pm,Module-Runtime-0.014.tar.gz,Module-Runtime-0.014))
 $(eval $(call InstallPerlPM,Try/Tiny.pm,Try-Tiny-0.22.tar.gz,Try-Tiny-0.22))
 $(eval $(call InstallPerlPM,Math/Bezier.pm,Math-Bezier-0.01.tar.gz,Math-Bezier-0.01))
 $(eval $(call InstallPerlPM,Math/VecStat.pm,Math-VecStat-0.08.tar.gz,Math-VecStat-0.08))
 $(eval $(call InstallPerlPM,Regexp/Common.pm,Regexp-Common-2013031301.tar.gz,Regexp-Common-2013031301))
 $(eval $(call InstallPerlPM,Set/IntSpan.pm,Set-IntSpan-1.19.tar.gz,Set-IntSpan-1.19))
 $(eval $(call InstallPerlPM,x86_64-linux-thread-multi/Time/HiRes.pm,Time-HiRes-1.9726.tar.gz,Time-HiRes-1.9726))
 $(eval $(call InstallPerlPM,Text/Format.pm,Text-Format-0.59.tar.gz,Text-Format-0.59))
 $(eval $(call InstallPerlPM,Math/BigInt.pm,Math-BigInt-1.9993.tar.gz,Math-BigInt-1.9993))
 $(eval $(call InstallPerlPM,Config/General.pm,Config-General-2.56.tar.gz,Config-General-2.56))
 $(eval $(call InstallPerlPM,x86_64-linux-thread-multi/Storable.pm,Storable-2.51.tar.gz,Storable-2.51))
 $(eval $(call InstallPerlPM,Number/Format.pm,Number-Format-1.73.tar.gz,Number-Format-1.73))
 $(eval $(call InstallPerlPM,Math/Round.pm,Math-Round-0.07.tar.gz,Math-Round-0.07))
 $(eval $(call InstallPerlPM,x86_64-linux-thread-multi/Clone.pm,Clone-0.38.tar.gz,Clone-0.38))
 $(eval $(call InstallPerlPM,Pod/Usage.pm,Pod-Usage-1.67.tar.gz,Pod-Usage-1.67))
 $(eval $(call InstallPerlPM,Text/Balanced.pm,Text-Balanced-2.03.tar.gz,Text-Balanced-2.03))
 $(eval $(call InstallPerlPM,Carp.pm,Carp-1.36.tar.gz,Carp-1.36))
 $(eval $(call InstallPerlPM,Parallel/ForkManager.pm,Parallel-ForkManager-1.13.tar.gz,Parallel-ForkManager-1.13))
 $(eval $(call InstallPerlPM,Module/Implementation.pm,Module-Implementation-0.09.tar.gz $(INSTALL_DIR)/lib/perl5/Module/Runtime.pm $(INSTALL_DIR)/lib/perl5/Try/Tiny.pm,Module-Implementation-0.09))
 $(eval $(call InstallPerlPM,Statistics/Basic.pm,Statistics-Basic-1.6611.tar.gz $(INSTALL_DIR)/lib/perl5/Number/Format.pm,Statistics-Basic-1.6611))

 $(eval $(call InstallPerlPM2,Memoize.pm,Memoize-1.03.tgz,Memoize-1.03))
 $(eval $(call InstallPerlPM3,Readonly.pm ,Readonly-2.00.tar.gz,Readonly-2.00))
 $(eval $(call InstallPerlPM3,x86_64-linux-thread-multi/Params/Validate.pm,Params-Validate-1.26.tar.gz $(INSTALL_DIR)/lib/perl5/Module/Implementation.pm $(INSTALL_DIR)/lib/perl5/Test/Fatal.pm $(INSTALL_DIR)/lib/perl5/Test/Requires.pm,Params-Validate-1.26))

 clean:
     @rm -rf $(INSTALL_DIR)

  • Facilitates modularization and clear process logic.

  • Can be combined with PBS/SGE for cluster grid computing.

     .PHONY: all
 all:fastq1.fastq.gz.zip fastq2.fastq.gz.zip

 define FastQC
 $1_fastqc.zip \$1_fastqc.html : $1.qc.intermediate
 .INTERMEDIATE:$1.qc.intermediate
 $1.qc.intermediate:$indir/\$2
     cd $(OD) && \
     echo "cd $(OD) && fastqc -o ./ --extract -f fastq -t 8 -q $indir/\$2 "\
     > $(OD)/$1.qc.sh && \
     qsub -cwd -sync y -q all.q -l ncpu 8 $1.qc.sh
 endef

 $(eval $(call FastQC,fastq1_Prefix,fastq1.fastq.gz))
 $(eval $(call FastQC,fastq2_Prefix,fastq2.fastq.gz))

 clean:
     rm -rf fastq1.fastq.gz.zip fastq2.fastq.gz.zip fastq1.fastq.gz.html fastq2.fastq.gz.html
     OD=$(CURDIR)
 .PHONY: all
 all: TEST1_test TEST2_test TEST3_test TEST4_test TEST5_test 

 define test
 $1_test :
     cd $(OD) && \
     echo "cd $(OD) && hostname > $(OD)/$1_test"\
     > $(OD)/$1.test.sh && \
     qsub -V -cwd -sync y -q all.q $(OD)/$1.test.sh
 endef

 $(eval $(call test,TEST1))
 $(eval $(call test,TEST2))
 $(eval $(call test,TEST3))
 $(eval $(call test,TEST4))
 $(eval $(call test,TEST5))

 clean:
     rm -rf TEST*test*
     make -j 2 -f Fastqc.make
 make -j 5 -f test.make

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