X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=sources%2Freadseq%2FMake.ncbi;fp=sources%2Freadseq%2FMake.ncbi;h=f6df5af6d9185dc87d00737afcb4454d07629297;hb=9aa768067094f24f46f273077f867348e6143711;hp=0000000000000000000000000000000000000000;hpb=eb3001dc41bf6cd46e20fd13fe3efbe9dedf6013;p=jpred.git diff --git a/sources/readseq/Make.ncbi b/sources/readseq/Make.ncbi new file mode 100644 index 0000000..f6df5af --- /dev/null +++ b/sources/readseq/Make.ncbi @@ -0,0 +1,110 @@ +# +# 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=/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 +