112 lines
3.2 KiB
Makefile
112 lines
3.2 KiB
Makefile
|
#
|
||
|
|
# Unix Makefile for readseq
|
||
|
|
# to use, command me:
|
||
|
|
# % make -- or --
|
||
|
|
# % make CC=your-c-compiler-name
|
||
|
|
#
|
||
|
|
|
||
|
|
# pick an ANSI C compiler (the default Sun CC is not ANSI)
|
||
|
|
CC=gcc # Gnu C Compiler
|
||
|
|
#CC=cc # SGI Irix
|
||
|
|
#CC=vcc # some DEC Ultrix
|
||
|
|
|
||
|
|
CFLAGS=
|
||
|
|
#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
|
||
|
|
|
||
|
|
SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
|
||
|
|
DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
|
||
|
|
|
||
|
|
|
||
|
|
# NCBI toolkit support for ASN.1 reader
|
||
|
|
|
||
|
|
# this is path to NCBI toolkit, you must set for your system:
|
||
|
|
NCBI=
|
||
|
|
#NCBI=/bio/mb/ncbi
|
||
|
|
#
|
||
|
|
OTHERLIBS=-lm
|
||
|
|
LIB1=-lncbi
|
||
|
|
LIB2=-lncbiobj
|
||
|
|
LIB3=-lncbicdr
|
||
|
|
LIB4=-lvibrant
|
||
|
|
INCPATH=$(NCBI)/include
|
||
|
|
LIBPATH=$(NCBI)/lib
|
||
|
|
NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
|
||
|
|
NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
|
||
|
|
NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
|
||
|
|
|
||
|
|
|
||
|
|
all: build test
|
||
|
|
|
||
|
|
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)
|
||
|
|
|
||
|
|
test: $(SOURCES) readseq
|
||
|
|
@echo ""
|
||
|
|
@echo "Test for general read/write of all chars:"
|
||
|
|
./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
|
||
|
|
-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
|
||
|
|
-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 "Expect differences in the header lines due to"
|
||
|
|
@echo "different format headers. If any sequence lines"
|
||
|
|
@echo "differ, or if the checksums differ, there is a problem."
|
||
|
|
@echo "----------------------"
|
||
|
|
@echo ""
|
||
|
|
@echo "To clean up test files, command me:"
|
||
|
|
@echo " make clean"
|
||
|
|
|
||
|
|
|
||
|
|
clean:
|
||
|
|
rm -f *.o core test.*
|
||
|
|
|
||
|
|
shar:
|
||
|
|
@echo "shell archiving files..."
|
||
|
|
-rm -f readseq*.shar
|
||
|
|
mkdir readseqd
|
||
|
|
cp $(SOURCES) readseqd
|
||
|
|
cp $(DOCS) readseqd
|
||
|
|
shar -v readseqd > readseq.shar
|
||
|
|
rm -rf readseqd
|
||
|
|
|