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|
#! /bin/sh /usr/share/dpatch/dpatch-run
## 20_Makefile.dpatch by <tille@debian.org>
##
## All lines beginning with `## DP:' are a description of the patch.
## DP: Enhanced Makefile
@DPATCH@
--- readseq-1/Makefile.orig 1992-12-30 01:00:00.000000000 +0100
+++ readseq-1/Makefile 2007-11-17 21:31:39.000000000 +0100
@@ -10,7 +10,7 @@
#CC=cc # SGI Irix
#CC=vcc # some DEC Ultrix
-CFLAGS=
+CFLAGS= -g -O2
#CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
# instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
@@ -29,63 +29,66 @@
LIB2=-lncbiobj
LIB3=-lncbicdr
LIB4=-lvibrant
-INCPATH=$(NCBI)/include
-LIBPATH=$(NCBI)/lib
+LIB5=-lncbimmdb -lncbiid1 -lnetcli
+LIB6=-lncbiacc
+LIB7=-lncbitool
+INCPATH=/usr/include/ncbi
+#LIBPATH=$(NCBI)/lib
NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
-NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
-NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
+NLDFLAGS=-I$(INCPATH)
+NLIBS=$(LIB1) $(LIB2) $(LIB3) $(LIB6) $(LIB7) $(LIB5) $(OTHERLIBS)
+ARBFLAGS=-DARB
+all: build
-all: build test
-
-build: $(SOURCES)
- @echo "Compiling readseq..."
- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
+#build: $(SOURCES)
+# @echo "Compiling readseq..."
+# $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
# if using NCBI, uncomment these lines in place of build: above
-#build: $(SOURCES)
-# @echo "Compiling readseq with NCBI toolkit support...";
-# $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
+build: $(SOURCES)
+ @echo "Compiling readseq with NCBI toolkit support and ARB patches";
+ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
-test: $(SOURCES) readseq
+test:
@echo ""
@echo "Test for general read/write of all chars:"
- ./readseq -p alphabet.std -otest.alpha
+ readseq -p alphabet.std -otest.alpha
-diff test.alpha alphabet.std
@echo ""
@echo "Test for valid format conversions:"
- ./readseq -v -p -f=ig nucleic.std -otest.ig
- ./readseq -v -p -f=gb test.ig -otest.gb
- ./readseq -v -p -f=nbrf test.gb -otest.nbrf
- ./readseq -v -p -f=embl test.nbrf -otest.embl
- ./readseq -v -p -f=gcg test.embl -otest.gcg
- ./readseq -v -p -f=strider test.gcg -otest.strider
- ./readseq -v -p -f=fitch test.strider -otest.fitch
- ./readseq -v -p -f=fasta test.fitch -otest.fasta
- ./readseq -v -p -f=pir test.fasta -otest.pir
- ./readseq -v -p -f=ig test.pir -otest.ig-b
+ readseq -v -p -f=ig nucleic.std -otest.ig
+ readseq -v -p -f=gb test.ig -otest.gb
+ readseq -v -p -f=nbrf test.gb -otest.nbrf
+ readseq -v -p -f=embl test.nbrf -otest.embl
+ readseq -v -p -f=gcg test.embl -otest.gcg
+ readseq -v -p -f=strider test.gcg -otest.strider
+ readseq -v -p -f=fitch test.strider -otest.fitch
+ readseq -v -p -f=fasta test.fitch -otest.fasta
+ readseq -v -p -f=pir test.fasta -otest.pir
+ readseq -v -p -f=ig test.pir -otest.ig-b
-diff test.ig test.ig-b
@echo ""
@echo "Test for multiple-sequence format conversions:"
- ./readseq -p -f=ig multi.std -otest.m-ig
- ./readseq -p -f=gb test.m-ig -otest.m-gb
- ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
- ./readseq -p -f=embl test.m-nbrf -otest.m-embl
- ./readseq -p -f=fasta test.m-embl -otest.m-fasta
- ./readseq -p -f=pir test.m-fasta -otest.m-pir
- ./readseq -p -f=msf test.m-pir -otest.m-msf
- ./readseq -p -f=paup test.m-msf -otest.m-paup
- ./readseq -p -f=ig test.m-paup -otest.m-ig-b
+ readseq -p -f=ig multi.std -otest.m-ig
+ readseq -p -f=gb test.m-ig -otest.m-gb
+ readseq -p -f=nbrf test.m-gb -otest.m-nbrf
+ readseq -p -f=embl test.m-nbrf -otest.m-embl
+ readseq -p -f=fasta test.m-embl -otest.m-fasta
+ readseq -p -f=pir test.m-fasta -otest.m-pir
+ readseq -p -f=msf test.m-pir -otest.m-msf
+ readseq -p -f=paup test.m-msf -otest.m-paup
+ readseq -p -f=ig test.m-paup -otest.m-ig-b
-diff test.m-ig test.m-ig-b
#
# if using NCBI, uncomment these lines
-# @echo ""
-# @echo "Test of NCBI ASN.1 conversions:"
-# ./readseq -p -f=asn test.m-ig -otest.m-asn
-# ./readseq -p -f=ig test.m-asn -otest.m-ig-c
-# -diff test.m-ig test.m-ig-c
+ @echo ""
+ @echo "Test of NCBI ASN.1 conversions:"
+ readseq -p -f=asn test.m-ig -otest.m-asn
+ readseq -p -f=ig test.m-asn -otest.m-ig-c
+ -diff test.m-ig test.m-ig-c
#
@echo ""
@echo "Expect differences in the header lines due to"
@@ -97,8 +100,13 @@
@echo " make clean"
+install:
+ install readseq $(DESTDIR)/usr/bin
+ install *.std $(DESTDIR)/usr/share/doc/readseq/tests
+ install Makefile $(DESTDIR)/usr/share/doc/readseq/tests
+
clean:
- rm -f *.o core test.*
+ rm -f *.o core test.* readseq
shar:
@echo "shell archiving files..."
@@ -109,3 +117,7 @@
shar -v readseqd > readseq.shar
rm -rf readseqd
+
+
+
+
|
