112 lines
3.2 KiB
Makefile
112 lines
3.2 KiB
Makefile
#
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# Unix Makefile for readseq
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# to use, command me:
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# % make -- or --
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# % make CC=your-c-compiler-name
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#
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# pick an ANSI C compiler (the default Sun CC is not ANSI)
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CC=gcc # Gnu C Compiler
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#CC=cc # SGI Irix
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#CC=vcc # some DEC Ultrix
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CFLAGS=
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#CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
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# instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
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SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
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DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
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# NCBI toolkit support for ASN.1 reader
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# this is path to NCBI toolkit, you must set for your system:
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NCBI=
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#NCBI=/bio/mb/ncbi
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#
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OTHERLIBS=-lm
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LIB1=-lncbi
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LIB2=-lncbiobj
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LIB3=-lncbicdr
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LIB4=-lvibrant
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INCPATH=$(NCBI)/include
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LIBPATH=$(NCBI)/lib
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NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
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NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
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NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
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all: build test
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build: $(SOURCES)
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@echo "Compiling readseq..."
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$(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
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# if using NCBI, uncomment these lines in place of build: above
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#build: $(SOURCES)
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# @echo "Compiling readseq with NCBI toolkit support...";
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# $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
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test: $(SOURCES) readseq
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@echo ""
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@echo "Test for general read/write of all chars:"
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./readseq -p alphabet.std -otest.alpha
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-diff test.alpha alphabet.std
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@echo ""
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@echo "Test for valid format conversions:"
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./readseq -v -p -f=ig nucleic.std -otest.ig
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./readseq -v -p -f=gb test.ig -otest.gb
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./readseq -v -p -f=nbrf test.gb -otest.nbrf
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./readseq -v -p -f=embl test.nbrf -otest.embl
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./readseq -v -p -f=gcg test.embl -otest.gcg
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./readseq -v -p -f=strider test.gcg -otest.strider
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./readseq -v -p -f=fitch test.strider -otest.fitch
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./readseq -v -p -f=fasta test.fitch -otest.fasta
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./readseq -v -p -f=pir test.fasta -otest.pir
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./readseq -v -p -f=ig test.pir -otest.ig-b
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-diff test.ig test.ig-b
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@echo ""
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@echo "Test for multiple-sequence format conversions:"
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./readseq -p -f=ig multi.std -otest.m-ig
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./readseq -p -f=gb test.m-ig -otest.m-gb
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./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
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./readseq -p -f=embl test.m-nbrf -otest.m-embl
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./readseq -p -f=fasta test.m-embl -otest.m-fasta
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./readseq -p -f=pir test.m-fasta -otest.m-pir
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./readseq -p -f=msf test.m-pir -otest.m-msf
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./readseq -p -f=paup test.m-msf -otest.m-paup
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./readseq -p -f=ig test.m-paup -otest.m-ig-b
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-diff test.m-ig test.m-ig-b
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#
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# if using NCBI, uncomment these lines
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# @echo ""
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# @echo "Test of NCBI ASN.1 conversions:"
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# ./readseq -p -f=asn test.m-ig -otest.m-asn
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# ./readseq -p -f=ig test.m-asn -otest.m-ig-c
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# -diff test.m-ig test.m-ig-c
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#
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@echo ""
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@echo "Expect differences in the header lines due to"
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@echo "different format headers. If any sequence lines"
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@echo "differ, or if the checksums differ, there is a problem."
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@echo "----------------------"
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@echo ""
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@echo "To clean up test files, command me:"
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@echo " make clean"
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clean:
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rm -f *.o core test.*
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shar:
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@echo "shell archiving files..."
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-rm -f readseq*.shar
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mkdir readseqd
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cp $(SOURCES) readseqd
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cp $(DOCS) readseqd
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shar -v readseqd > readseq.shar
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rm -rf readseqd
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