2 # Unix Makefile for readseq
5 # % make CC=your-c-compiler-name
8 # pick an ANSI C compiler (the default Sun CC is not ANSI)
9 CC=gcc # Gnu C Compiler
11 #CC=vcc # some DEC Ultrix
14 #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
15 # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
17 SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
18 DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
21 # NCBI toolkit support for ASN.1 reader
23 # this is path to NCBI toolkit, you must set for your system:
32 INCPATH=$(NCBI)/include
34 NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
35 NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
36 NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
42 @echo "Compiling readseq..."
43 $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
45 # if using NCBI, uncomment these lines in place of build: above
47 # @echo "Compiling readseq with NCBI toolkit support...";
48 # $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
50 test: $(SOURCES) readseq
52 @echo "Test for general read/write of all chars:"
53 ./readseq -p alphabet.std -otest.alpha
54 -diff test.alpha alphabet.std
57 @echo "Test for valid format conversions:"
58 ./readseq -v -p -f=ig nucleic.std -otest.ig
59 ./readseq -v -p -f=gb test.ig -otest.gb
60 ./readseq -v -p -f=nbrf test.gb -otest.nbrf
61 ./readseq -v -p -f=embl test.nbrf -otest.embl
62 ./readseq -v -p -f=gcg test.embl -otest.gcg
63 ./readseq -v -p -f=strider test.gcg -otest.strider
64 ./readseq -v -p -f=fitch test.strider -otest.fitch
65 ./readseq -v -p -f=fasta test.fitch -otest.fasta
66 ./readseq -v -p -f=pir test.fasta -otest.pir
67 ./readseq -v -p -f=ig test.pir -otest.ig-b
68 -diff test.ig test.ig-b
71 @echo "Test for multiple-sequence format conversions:"
72 ./readseq -p -f=ig multi.std -otest.m-ig
73 ./readseq -p -f=gb test.m-ig -otest.m-gb
74 ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
75 ./readseq -p -f=embl test.m-nbrf -otest.m-embl
76 ./readseq -p -f=fasta test.m-embl -otest.m-fasta
77 ./readseq -p -f=pir test.m-fasta -otest.m-pir
78 ./readseq -p -f=msf test.m-pir -otest.m-msf
79 ./readseq -p -f=paup test.m-msf -otest.m-paup
80 ./readseq -p -f=ig test.m-paup -otest.m-ig-b
81 -diff test.m-ig test.m-ig-b
83 # if using NCBI, uncomment these lines
85 # @echo "Test of NCBI ASN.1 conversions:"
86 # ./readseq -p -f=asn test.m-ig -otest.m-asn
87 # ./readseq -p -f=ig test.m-asn -otest.m-ig-c
88 # -diff test.m-ig test.m-ig-c
91 @echo "Expect differences in the header lines due to"
92 @echo "different format headers. If any sequence lines"
93 @echo "differ, or if the checksums differ, there is a problem."
94 @echo "----------------------"
96 @echo "To clean up test files, command me:"
101 rm -f *.o core test.*
104 @echo "shell archiving files..."
107 cp $(SOURCES) readseqd
109 shar -v readseqd > readseq.shar