sources/readseq/Make.ncbi

   1 #
   2 # Unix Makefile for readseq
   3 # to use, command me:
   4 #  %  make       -- or --
   5 #  %  make CC=your-c-compiler-name
   6 #
   7
   8 # pick an ANSI C compiler (the default Sun CC is not ANSI)
   9 CC=gcc  # Gnu C Compiler
  10 #CC=cc  # SGI Irix
  11 #CC=vcc # some DEC Ultrix
  12
  13 CFLAGS=
  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
  16
  17 SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
  18 DOCS= Readme readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
  19
  20
  21 # NCBI toolkit support for ASN.1 reader
  22
  23 # this is path to NCBI toolkit, you must set for your system:
  24 NCBI=/bio/mb/ncbi
  25 #
  26 OTHERLIBS=-lm
  27 LIB1=-lncbi
  28 LIB2=-lncbiobj
  29 LIB3=-lncbicdr
  30 LIB4=-lvibrant
  31 INCPATH=$(NCBI)/include
  32 LIBPATH=$(NCBI)/lib
  33 NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
  34 NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
  35 NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
  36
  37
  38 all: build test
  39
  40 #build: $(SOURCES)
  41 #       @echo "Compiling readseq..."
  42 #       $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
  43
  44 # if using NCBI, uncomment these lines in place of build: above
  45 build: $(SOURCES)
  46         @echo "Compiling readseq with NCBI toolkit support...";
  47         $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
  48
  49 test: $(SOURCES) readseq
  50         @echo ""
  51         @echo "Test for general read/write of all chars:"
  52         ./readseq -p alphabet.std -otest.alpha
  53         -diff test.alpha alphabet.std
  54
  55         @echo ""
  56         @echo "Test for valid format conversions:"
  57         ./readseq -v -p -f=ig   nucleic.std -otest.ig
  58         ./readseq -v -p -f=gb   test.ig     -otest.gb
  59         ./readseq -v -p -f=nbrf test.gb     -otest.nbrf
  60         ./readseq -v -p -f=embl test.nbrf   -otest.embl
  61         ./readseq -v -p -f=gcg  test.embl   -otest.gcg
  62         ./readseq -v -p -f=strider test.gcg -otest.strider
  63         ./readseq -v -p -f=fitch test.strider -otest.fitch
  64         ./readseq -v -p -f=fasta test.fitch -otest.fasta
  65         ./readseq -v -p -f=pir  test.fasta  -otest.pir
  66         ./readseq -v -p -f=ig   test.pir    -otest.ig-b
  67         -diff test.ig test.ig-b
  68
  69         @echo ""
  70         @echo "Test for multiple-sequence format conversions:"
  71         ./readseq -p -f=ig    multi.std   -otest.m-ig
  72         ./readseq -p -f=gb    test.m-ig   -otest.m-gb
  73         ./readseq -p -f=nbrf  test.m-gb   -otest.m-nbrf
  74         ./readseq -p -f=embl  test.m-nbrf -otest.m-embl
  75         ./readseq -p -f=fasta test.m-embl -otest.m-fasta
  76         ./readseq -p -f=pir   test.m-fasta -otest.m-pir
  77         ./readseq -p -f=msf   test.m-pir  -otest.m-msf
  78         ./readseq -p -f=paup  test.m-msf  -otest.m-paup
  79         ./readseq -p -f=ig    test.m-paup -otest.m-ig-b
  80         -diff test.m-ig test.m-ig-b
  81 #
  82 # if using NCBI, uncomment these lines
  83         @echo ""
  84         @echo "Test of NCBI ASN.1 conversions:"
  85         ./readseq -p -f=asn test.m-ig  -otest.m-asn
  86         ./readseq -p -f=ig  test.m-asn -otest.m-ig-c
  87         -diff test.m-ig test.m-ig-c
  88 #
  89         @echo ""
  90         @echo "Expect differences in the header lines due to"
  91         @echo "different format headers.  If any sequence lines"
  92         @echo "differ, or if the checksums differ, there is a problem."
  93         @echo "----------------------"
  94         @echo ""
  95         @echo "To clean up test files, command me:"
  96         @echo "    make clean"
  97
  98
  99 clean:
 100         rm -f *.o core test.*
 101
 102 shar:
 103         @echo "shell archiving files..."
 104         -rm -f readseq*.shar
 105         mkdir readseqd
 106         cp $(SOURCES) readseqd
 107         cp $(DOCS) readseqd
 108         shar -v readseqd > readseq.shar
 109         rm -rf readseqd
 110