diff --git a/Makefile b/Makefile deleted file mode 100644 index 812ab60..0000000 --- a/Makefile +++ /dev/null @@ -1,423 +0,0 @@ -# -*- makefile -*- -# just make headings for each thing and put the headings -# on the line for ALL -PROJECTDIR = . -BINDIR = $(PROJECTDIR) - -CC = gcc -CPPC = g++ -CFLAGS = -O3 -g -Wall -LDFLAGS = -lm - - -BINARIES = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs -DEPEND_FILES = *.cc *.c *.h -CLEANABLE_FILES = *.o *~ $(BINARIES) -CLEANABLE_FILES += debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 - -ALL = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists \ - tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs - -.SUFFIXES: .cc .c - -.c.o: - $(CC) $(CFLAGS) -c $*.c -o $*.o - -.cc.o: - $(CPPC) $(CFLAGS) -c $*.cc -o $*.o - -all: $(ALL) - -tigr-adjust: adjust.o delcher.o - $(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS) - -tigr-anomaly: anomaly.o delcher.o gene.o - $(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS) - -tigr-build-icm: build-icm.o misc.o - $(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS) - -tigr-check: check.o delcher.o - $(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS) - -tigr-codon-usage: codon-usage.o delcher.o gene.o - $(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS) - -tigr-compare-lists: compare-lists.o delcher.o - $(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS) - -tigr-extract: extract.o delcher.o - $(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS) - -tigr-generate: generate.o delcher.o gene.o - $(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS) - -tigr-get-len: get-len.o delcher.o - $(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS) - -tigr-get-putative: get-putative.o delcher.o - $(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS) - -tigr-glimmer2: glimmer2.o delcher.o gene.o rnabin.o - $(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS) - -tigr-long-orfs: long-orfs.o delcher.o gene.o - $(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS) - -tigr-rnabin: rnabin.o delcher.o - $(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS) - -depend: - makedepend $(DEPEND_FILES) - -clean: - /bin/rm -f $(CLEANABLE_FILES) - -# DO NOT DELETE THIS LINE -- make depend depends on it. - -adjust.o: delcher.h /usr/include/stdio.h /usr/include/features.h -adjust.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -adjust.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -adjust.o: /usr/include/bits/typesizes.h /usr/include/libio.h -adjust.o: /usr/include/_G_config.h /usr/include/wchar.h -adjust.o: /usr/include/bits/wchar.h /usr/include/gconv.h -adjust.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -adjust.o: /usr/include/stdlib.h /usr/include/math.h -adjust.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -adjust.o: /usr/include/bits/mathcalls.h /usr/include/string.h -adjust.o: /usr/include/ctype.h /usr/include/endian.h -adjust.o: /usr/include/bits/endian.h /usr/include/limits.h -adjust.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -adjust.o: /usr/include/errno.h /usr/include/bits/errno.h -adjust.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -adjust.o: /usr/include/asm-generic/errno.h -adjust.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -adjust.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -anomaly.o: delcher.h /usr/include/stdio.h /usr/include/features.h -anomaly.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -anomaly.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -anomaly.o: /usr/include/bits/typesizes.h /usr/include/libio.h -anomaly.o: /usr/include/_G_config.h /usr/include/wchar.h -anomaly.o: /usr/include/bits/wchar.h /usr/include/gconv.h -anomaly.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -anomaly.o: /usr/include/stdlib.h /usr/include/math.h -anomaly.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -anomaly.o: /usr/include/bits/mathcalls.h /usr/include/string.h -anomaly.o: /usr/include/ctype.h /usr/include/endian.h -anomaly.o: /usr/include/bits/endian.h /usr/include/limits.h -anomaly.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -anomaly.o: /usr/include/errno.h /usr/include/bits/errno.h -anomaly.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -anomaly.o: /usr/include/asm-generic/errno.h -anomaly.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -anomaly.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h -check.o: delcher.h /usr/include/stdio.h /usr/include/features.h -check.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -check.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -check.o: /usr/include/bits/typesizes.h /usr/include/libio.h -check.o: /usr/include/_G_config.h /usr/include/wchar.h -check.o: /usr/include/bits/wchar.h /usr/include/gconv.h -check.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -check.o: /usr/include/stdlib.h /usr/include/math.h -check.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -check.o: /usr/include/bits/mathcalls.h /usr/include/string.h -check.o: /usr/include/ctype.h /usr/include/endian.h -check.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h -check.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h -check.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -check.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -check.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -check.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -codon-usage.o: delcher.h /usr/include/stdio.h /usr/include/features.h -codon-usage.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -codon-usage.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -codon-usage.o: /usr/include/bits/typesizes.h /usr/include/libio.h -codon-usage.o: /usr/include/_G_config.h /usr/include/wchar.h -codon-usage.o: /usr/include/bits/wchar.h /usr/include/gconv.h -codon-usage.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -codon-usage.o: /usr/include/stdlib.h /usr/include/math.h -codon-usage.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -codon-usage.o: /usr/include/bits/mathcalls.h /usr/include/string.h -codon-usage.o: /usr/include/ctype.h /usr/include/endian.h -codon-usage.o: /usr/include/bits/endian.h /usr/include/limits.h -codon-usage.o: /usr/include/time.h /usr/include/bits/time.h -codon-usage.o: /usr/include/assert.h /usr/include/errno.h -codon-usage.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -codon-usage.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -codon-usage.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -codon-usage.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -codon-usage.o: gene.h -compare-lists.o: delcher.h /usr/include/stdio.h /usr/include/features.h -compare-lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -compare-lists.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -compare-lists.o: /usr/include/bits/typesizes.h /usr/include/libio.h -compare-lists.o: /usr/include/_G_config.h /usr/include/wchar.h -compare-lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h -compare-lists.o: /usr/include/bits/stdio_lim.h -compare-lists.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h -compare-lists.o: /usr/include/math.h /usr/include/bits/huge_val.h -compare-lists.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h -compare-lists.o: /usr/include/string.h /usr/include/ctype.h -compare-lists.o: /usr/include/endian.h /usr/include/bits/endian.h -compare-lists.o: /usr/include/limits.h /usr/include/time.h -compare-lists.o: /usr/include/bits/time.h /usr/include/assert.h -compare-lists.o: /usr/include/errno.h /usr/include/bits/errno.h -compare-lists.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -compare-lists.o: /usr/include/asm-generic/errno.h -compare-lists.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -compare-lists.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -delcher.o: delcher.h /usr/include/stdio.h /usr/include/features.h -delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h -delcher.o: /usr/include/_G_config.h /usr/include/wchar.h -delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h -delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -delcher.o: /usr/include/stdlib.h /usr/include/math.h -delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h -delcher.o: /usr/include/ctype.h /usr/include/endian.h -delcher.o: /usr/include/bits/endian.h /usr/include/limits.h -delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -delcher.o: /usr/include/errno.h /usr/include/bits/errno.h -delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -delcher.o: /usr/include/asm-generic/errno.h -delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -extract.o: delcher.h /usr/include/stdio.h /usr/include/features.h -extract.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -extract.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -extract.o: /usr/include/bits/typesizes.h /usr/include/libio.h -extract.o: /usr/include/_G_config.h /usr/include/wchar.h -extract.o: /usr/include/bits/wchar.h /usr/include/gconv.h -extract.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -extract.o: /usr/include/stdlib.h /usr/include/math.h -extract.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -extract.o: /usr/include/bits/mathcalls.h /usr/include/string.h -extract.o: /usr/include/ctype.h /usr/include/endian.h -extract.o: /usr/include/bits/endian.h /usr/include/limits.h -extract.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -extract.o: /usr/include/errno.h /usr/include/bits/errno.h -extract.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -extract.o: /usr/include/asm-generic/errno.h -extract.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -extract.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -gene.o: delcher.h /usr/include/stdio.h /usr/include/features.h -gene.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -gene.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -gene.o: /usr/include/bits/typesizes.h /usr/include/libio.h -gene.o: /usr/include/_G_config.h /usr/include/wchar.h -gene.o: /usr/include/bits/wchar.h /usr/include/gconv.h -gene.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -gene.o: /usr/include/stdlib.h /usr/include/math.h -gene.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -gene.o: /usr/include/bits/mathcalls.h /usr/include/string.h -gene.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h -gene.o: /usr/include/limits.h /usr/include/time.h /usr/include/bits/time.h -gene.o: /usr/include/assert.h /usr/include/errno.h /usr/include/bits/errno.h -gene.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -gene.o: /usr/include/asm-generic/errno.h -gene.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -gene.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h -generate.o: delcher.h /usr/include/stdio.h /usr/include/features.h -generate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -generate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -generate.o: /usr/include/bits/typesizes.h /usr/include/libio.h -generate.o: /usr/include/_G_config.h /usr/include/wchar.h -generate.o: /usr/include/bits/wchar.h /usr/include/gconv.h -generate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -generate.o: /usr/include/stdlib.h /usr/include/math.h -generate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -generate.o: /usr/include/bits/mathcalls.h /usr/include/string.h -generate.o: /usr/include/ctype.h /usr/include/endian.h -generate.o: /usr/include/bits/endian.h /usr/include/limits.h -generate.o: /usr/include/time.h /usr/include/bits/time.h -generate.o: /usr/include/assert.h /usr/include/errno.h -generate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -generate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -generate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -generate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h -generate.o: icm.h -get-len.o: delcher.h /usr/include/stdio.h /usr/include/features.h -get-len.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -get-len.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -get-len.o: /usr/include/bits/typesizes.h /usr/include/libio.h -get-len.o: /usr/include/_G_config.h /usr/include/wchar.h -get-len.o: /usr/include/bits/wchar.h /usr/include/gconv.h -get-len.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -get-len.o: /usr/include/stdlib.h /usr/include/math.h -get-len.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -get-len.o: /usr/include/bits/mathcalls.h /usr/include/string.h -get-len.o: /usr/include/ctype.h /usr/include/endian.h -get-len.o: /usr/include/bits/endian.h /usr/include/limits.h -get-len.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -get-len.o: /usr/include/errno.h /usr/include/bits/errno.h -get-len.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -get-len.o: /usr/include/asm-generic/errno.h -get-len.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -get-len.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -get-putative.o: delcher.h /usr/include/stdio.h /usr/include/features.h -get-putative.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -get-putative.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -get-putative.o: /usr/include/bits/typesizes.h /usr/include/libio.h -get-putative.o: /usr/include/_G_config.h /usr/include/wchar.h -get-putative.o: /usr/include/bits/wchar.h /usr/include/gconv.h -get-putative.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -get-putative.o: /usr/include/stdlib.h /usr/include/math.h -get-putative.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -get-putative.o: /usr/include/bits/mathcalls.h /usr/include/string.h -get-putative.o: /usr/include/ctype.h /usr/include/endian.h -get-putative.o: /usr/include/bits/endian.h /usr/include/limits.h -get-putative.o: /usr/include/time.h /usr/include/bits/time.h -get-putative.o: /usr/include/assert.h /usr/include/errno.h -get-putative.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -get-putative.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -get-putative.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -get-putative.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -glimmer2.o: delcher.h /usr/include/stdio.h /usr/include/features.h -glimmer2.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -glimmer2.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -glimmer2.o: /usr/include/bits/typesizes.h /usr/include/libio.h -glimmer2.o: /usr/include/_G_config.h /usr/include/wchar.h -glimmer2.o: /usr/include/bits/wchar.h /usr/include/gconv.h -glimmer2.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -glimmer2.o: /usr/include/stdlib.h /usr/include/math.h -glimmer2.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -glimmer2.o: /usr/include/bits/mathcalls.h /usr/include/string.h -glimmer2.o: /usr/include/ctype.h /usr/include/endian.h -glimmer2.o: /usr/include/bits/endian.h /usr/include/limits.h -glimmer2.o: /usr/include/time.h /usr/include/bits/time.h -glimmer2.o: /usr/include/assert.h /usr/include/errno.h -glimmer2.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -glimmer2.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -glimmer2.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -glimmer2.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h -glimmer2.o: icm.h -long-orfs.o: delcher.h /usr/include/stdio.h /usr/include/features.h -long-orfs.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -long-orfs.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -long-orfs.o: /usr/include/bits/typesizes.h /usr/include/libio.h -long-orfs.o: /usr/include/_G_config.h /usr/include/wchar.h -long-orfs.o: /usr/include/bits/wchar.h /usr/include/gconv.h -long-orfs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -long-orfs.o: /usr/include/stdlib.h /usr/include/math.h -long-orfs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -long-orfs.o: /usr/include/bits/mathcalls.h /usr/include/string.h -long-orfs.o: /usr/include/ctype.h /usr/include/endian.h -long-orfs.o: /usr/include/bits/endian.h /usr/include/limits.h -long-orfs.o: /usr/include/time.h /usr/include/bits/time.h -long-orfs.o: /usr/include/assert.h /usr/include/errno.h -long-orfs.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -long-orfs.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -long-orfs.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -long-orfs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -long-orfs.o: gene.h -rnabin.o: rnabin.h delcher.h /usr/include/stdio.h /usr/include/features.h -rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h -rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h -rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h -rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -rnabin.o: /usr/include/stdlib.h /usr/include/math.h -rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h -rnabin.o: /usr/include/ctype.h /usr/include/endian.h -rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h -rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h -rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -rnabin.o: /usr/include/asm-generic/errno.h -rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h -translate.o: delcher.h /usr/include/stdio.h /usr/include/features.h -translate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -translate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -translate.o: /usr/include/bits/typesizes.h /usr/include/libio.h -translate.o: /usr/include/_G_config.h /usr/include/wchar.h -translate.o: /usr/include/bits/wchar.h /usr/include/gconv.h -translate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -translate.o: /usr/include/stdlib.h /usr/include/math.h -translate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -translate.o: /usr/include/bits/mathcalls.h /usr/include/string.h -translate.o: /usr/include/ctype.h /usr/include/endian.h -translate.o: /usr/include/bits/endian.h /usr/include/limits.h -translate.o: /usr/include/time.h /usr/include/bits/time.h -translate.o: /usr/include/assert.h /usr/include/errno.h -translate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -translate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -translate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -translate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -build-icm.o: /usr/include/stdlib.h /usr/include/features.h -build-icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -build-icm.o: /usr/include/stdio.h /usr/include/bits/types.h -build-icm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -build-icm.o: /usr/include/libio.h /usr/include/_G_config.h -build-icm.o: /usr/include/wchar.h /usr/include/bits/wchar.h -build-icm.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h -build-icm.o: /usr/include/bits/sys_errlist.h /usr/include/math.h -build-icm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -build-icm.o: /usr/include/bits/mathcalls.h /usr/include/string.h -build-icm.o: /usr/include/ctype.h /usr/include/endian.h -build-icm.o: /usr/include/bits/endian.h /usr/include/unistd.h -build-icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -build-icm.o: build-icm.h misc.h -misc.o: /usr/include/stdlib.h /usr/include/features.h -misc.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -misc.o: /usr/include/stdio.h /usr/include/bits/types.h -misc.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -misc.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -misc.o: /usr/include/bits/wchar.h /usr/include/gconv.h -misc.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h misc.h -delcher.o: /usr/include/stdio.h /usr/include/features.h -delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h -delcher.o: /usr/include/_G_config.h /usr/include/wchar.h -delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h -delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -delcher.o: /usr/include/stdlib.h /usr/include/math.h -delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h -delcher.o: /usr/include/ctype.h /usr/include/endian.h -delcher.o: /usr/include/bits/endian.h /usr/include/limits.h -delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -delcher.o: /usr/include/errno.h /usr/include/bits/errno.h -delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -delcher.o: /usr/include/asm-generic/errno.h -delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -icm.o: delcher.h /usr/include/stdio.h /usr/include/features.h -icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -icm.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -icm.o: /usr/include/bits/typesizes.h /usr/include/libio.h -icm.o: /usr/include/_G_config.h /usr/include/wchar.h -icm.o: /usr/include/bits/wchar.h /usr/include/gconv.h -icm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -icm.o: /usr/include/stdlib.h /usr/include/math.h /usr/include/bits/huge_val.h -icm.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h -icm.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -icm.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h -icm.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h -icm.o: /usr/include/bits/errno.h /usr/include/linux/errno.h -icm.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h -icm.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -rnabin.o: delcher.h /usr/include/stdio.h /usr/include/features.h -rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h -rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h -rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h -rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -rnabin.o: /usr/include/stdlib.h /usr/include/math.h -rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h -rnabin.o: /usr/include/ctype.h /usr/include/endian.h -rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h -rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h -rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h -rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h -rnabin.o: /usr/include/asm-generic/errno.h -rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h -rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h diff --git a/debian/control b/debian/control index 1ce5836..95de184 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,7 @@ DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Andreas Tille -Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs +Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs, quilt Standards-Version: 3.7.3 Homepage: http://www.tigr.org/software/glimmer/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0 diff --git a/debian/dirs b/debian/dirs deleted file mode 100644 index e772481..0000000 --- a/debian/dirs +++ /dev/null @@ -1 +0,0 @@ -usr/bin diff --git a/debian/docs b/debian/docs index 7d94e9f..a5cef65 100644 --- a/debian/docs +++ b/debian/docs @@ -1,7 +1,2 @@ -README -ACKNOWLEDGEMENTS -changelog.gz -build-icm.readme -extract.readme -glimmer2.readme -long-orfs.readme +docs/notes.pdf +glim302notes.pdf diff --git a/debian/install b/debian/install index 7201b61..d4d6a16 100644 --- a/debian/install +++ b/debian/install @@ -1,13 +1,2 @@ -tigr-adjust usr/bin -tigr-anomaly usr/bin -tigr-build-icm usr/bin -tigr-check usr/bin -tigr-codon-usage usr/bin -tigr-compare-lists usr/bin -tigr-extract usr/bin -tigr-generate usr/bin -tigr-get-len usr/bin -tigr-get-putative usr/bin -tigr-glimmer2 usr/bin -tigr-long-orfs usr/bin -tigr-run-glimmer2 usr/bin +bin/* usr/bin +debian/tigr-run-glimmer3 usr/bin diff --git a/debian/patches/01_Makefile.patch b/debian/patches/01_Makefile.patch new file mode 100644 index 0000000..73b5141 --- /dev/null +++ b/debian/patches/01_Makefile.patch @@ -0,0 +1,10 @@ +--- /dev/null ++++ glimmer3.02/Makefile +@@ -0,0 +1,7 @@ ++all: ++ cd src; make ++ ++clean: ++ cd src; make clean ++ rm -f bin/* lib/* obj/* ++ diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..c3de10c --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +01_Makefile.patch diff --git a/debian/rules b/debian/rules index 01a5f03..0d4fdca 100755 --- a/debian/rules +++ b/debian/rules @@ -1,42 +1,10 @@ #!/usr/bin/make -f -# -*- makefile -*- -# Sample debian/rules that uses debhelper. -# GNU copyright 1997 to 1999 by Joey Hess. -# -# Modified to make a template file for a multi-binary package with separated -# build-arch and build-indep targets by Bill Allombert 2001 +# debian/rules for ncbi-epcr using cdbs +# Andreas Tille , GPL -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -.PHONY: clean - +include /usr/share/cdbs/1/rules/patchsys-quilt.mk include /usr/share/cdbs/1/rules/debhelper.mk -include /usr/share/cdbs/1/class/langcore.mk - -# This has to be exported to make some magic below work. -export DH_OPTIONS - -CFLAGS = -Wall -g -Wno-deprecated - -ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) - CFLAGS += -O0 -else - CFLAGS += -O2 -endif -ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) - INSTALL_PROGRAM += -s -endif - -package = tigr-glimmer - -build:build-arch-stamp build-indep-stamp -build-arch-stamp:: - dh_testdir - # Add here commands to compile the indep part of the package. - $(MAKE) all - ln -f run-glimmer2 tigr-run-glimmer2 - touch build-indep-stamp +include /usr/share/cdbs/1/class/makefile.mk MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 debian/tigr-long-orfs.1 @@ -45,14 +13,9 @@ .sgml.1: docbook-to-man $< > $@ -build-indep: $(MANPAGES) - gzip -9c CHANGELOG > changelog.gz - touch build-indep +clean:: + dh_clean $(MANPAGES) tigr-run-glimmer2 + rm -f bin/* lib/* obj/* -clean:: - dh_testdir - dh_testroot - rm -f build-arch-stamp build-indep-stamp configure-stamp changelog.gz - # Add here commands to clean up after the build process. - -$(MAKE) clean - dh_clean $(MANPAGES) tigr-run-glimmer2 +build/tigr-glimmer:: $(MANPAGES) + cd bin; for bin in `ls | grep -v "^tigr-"` ; do mv "$$bin" tigr-"$$bin" ; done diff --git a/debian/tigr-run-glimmer3 b/debian/tigr-run-glimmer3 new file mode 100755 index 0000000..6693fc3 --- /dev/null +++ b/debian/tigr-run-glimmer3 @@ -0,0 +1,17 @@ +#!/bin/sh +echo "run Glimmer3" +clear +echo "Genome is " $1 +echo "Find non-overlapping orfs in tmp.coord" +rm -f tmp.coord +tigr-long-orfs $1 | tigr-get-putative >tmp.coord +echo "Extract training sequences to tmp.train" +rm -f tmp.train +tigr-extract $1 tmp.coord >tmp.train +wc tmp.train +echo "Build interpolated context model in tmp.model" +rm -f tmp.model +tigr-build-icm tmp.model +echo "Predict genes with Glimmer3 with coordinates in g3.coord" +rm -f g3.coord +tigr-glimmer3 $1 tmp.model | tigr-get-putative >g3.coord diff --git a/delcher.h b/delcher.h deleted file mode 100644 index 44c8d85..0000000 --- a/delcher.h +++ /dev/null @@ -1,121 +0,0 @@ -// A. L. Delcher -// -// File: ANNOTATION/Glimmer/delcher.h -// Version: 2.03 3 Dec 2002 -// -// Copyright (c) 2002 by Arthur Delcher, Steven Salzberg, Simon -// Kasif, and Owen White. All rights reserved. Redistribution -// is not permitted without the express written permission of -// the authors. -// -// Common generic routines. -// - - -#ifndef __DELCHER_H_INCLUDED -#define __DELCHER_H_INCLUDED - - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -using namespace std; - -#define TRUE 1 -#define FALSE 0 -#ifndef EXIT_FAILURE - #define EXIT_FAILURE -1 -#endif -#ifndef EXIT_SUCCESS - #define EXIT_SUCCESS 0 -#endif - - -const int FASTA_WIDTH = 60; - // Max number of characters to print on a FASTA data line - - -const char * Commatize - (long int n); -void Fasta_Print - (FILE * fp, char * s, char * hdr); -void Fasta_Print_N - (FILE * fp, char * s, int n, char * hdr); -FILE * File_Open - (const char *, const char *); -double Percent - (double a, double b); -void * Safe_calloc - (size_t N, size_t Len, size_t line_num = 0); -void * Safe_malloc - (size_t Len, size_t line_num = 0); -void * Safe_realloc - (void * Q, size_t Len, size_t line_num = 0); - - -template - DT Max (DT, DT); -template - DT Min (DT, DT); -template - void Swap (DT &, DT &); - - -template -DT Max (DT A, DT B) - -// Return the larger of A and B . - - { - if (A > B) - return A; - else - return B; - } - - - -template -DT Min (DT A, DT B) - -// Return the smaller of A and B . - - { - if (A < B) - return A; - else - return B; - } - - - -template -void Swap (DT & A, DT & B) - -// Swap the values in A and B . - - { - DT Save; - - Save = A; - A = B; - B = Save; - - return; - } - - - -#endif diff --git a/run-glimmer2 b/run-glimmer2 deleted file mode 100755 index 92bdbd6..0000000 --- a/run-glimmer2 +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/sh -echo "run Glimmer2" -clear -echo "Genome is " $1 -echo "Find non-overlapping orfs in tmp.coord" -rm -f tmp.coord -tigr-long-orfs $1 | tigr-get-putative >tmp.coord -echo "Extract training sequences to tmp.train" -rm -f tmp.train -tigr-extract $1 tmp.coord >tmp.train -wc tmp.train -echo "Build interpolated context model in tmp.model" -rm -f tmp.model -tigr-build-icm tmp.model -echo "Predict genes with Glimmer2 with coordinates in g2.coord" -rm -f g2.coord -tigr-glimmer2 $1 tmp.model | tigr-get-putative >g2.coord