[med-svn] r1775 - in trunk/packages/tigr-glimmer/trunk: . debian debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Wed Apr 16 20:15:58 UTC 2008
Author: tille
Date: 2008-04-16 20:15:57 +0000 (Wed, 16 Apr 2008)
New Revision: 1775
Added:
trunk/packages/tigr-glimmer/trunk/debian/patches/
trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch
trunk/packages/tigr-glimmer/trunk/debian/patches/series
trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
Removed:
trunk/packages/tigr-glimmer/trunk/Makefile
trunk/packages/tigr-glimmer/trunk/debian/dirs
trunk/packages/tigr-glimmer/trunk/delcher.h
trunk/packages/tigr-glimmer/trunk/run-glimmer2
Modified:
trunk/packages/tigr-glimmer/trunk/debian/control
trunk/packages/tigr-glimmer/trunk/debian/docs
trunk/packages/tigr-glimmer/trunk/debian/install
trunk/packages/tigr-glimmer/trunk/debian/rules
Log:
Several changes to build packages of Glimmer3
Deleted: trunk/packages/tigr-glimmer/trunk/Makefile
===================================================================
--- trunk/packages/tigr-glimmer/trunk/Makefile 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/Makefile 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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
Modified: trunk/packages/tigr-glimmer/trunk/debian/control
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/control 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/debian/control 2008-04-16 20:15:57 UTC (rev 1775)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-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
Deleted: trunk/packages/tigr-glimmer/trunk/debian/dirs
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/dirs 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/debian/dirs 2008-04-16 20:15:57 UTC (rev 1775)
@@ -1 +0,0 @@
-usr/bin
Modified: trunk/packages/tigr-glimmer/trunk/debian/docs
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/docs 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/debian/docs 2008-04-16 20:15:57 UTC (rev 1775)
@@ -1,7 +1,2 @@
-README
-ACKNOWLEDGEMENTS
-changelog.gz
-build-icm.readme
-extract.readme
-glimmer2.readme
-long-orfs.readme
+docs/notes.pdf
+glim302notes.pdf
Modified: trunk/packages/tigr-glimmer/trunk/debian/install
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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
Added: trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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/*
++
Added: trunk/packages/tigr-glimmer/trunk/debian/patches/series
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/series (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/series 2008-04-16 20:15:57 UTC (rev 1775)
@@ -0,0 +1 @@
+01_Makefile.patch
Modified: trunk/packages/tigr-glimmer/trunk/debian/rules
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/rules 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/debian/rules 2008-04-16 20:15:57 UTC (rev 1775)
@@ -1,43 +1,11 @@
#!/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 <tille at debian.org>, 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
+include /usr/share/cdbs/1/class/makefile.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
-
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
.SUFFIXES: .1 .sgml
@@ -45,14 +13,9 @@
.sgml.1:
docbook-to-man $< > $@
-build-indep: $(MANPAGES)
- gzip -9c CHANGELOG > changelog.gz
- touch build-indep
-
clean::
- dh_testdir
- dh_testroot
- rm -f build-arch-stamp build-indep-stamp configure-stamp changelog.gz
- # Add here commands to clean up after the build process.
- -$(MAKE) clean
dh_clean $(MANPAGES) tigr-run-glimmer2
+ rm -f bin/* lib/* obj/*
+
+build/tigr-glimmer:: $(MANPAGES)
+ cd bin; for bin in `ls | grep -v "^tigr-"` ; do mv "$$bin" tigr-"$$bin" ; done
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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.train >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
Property changes on: trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/tigr-glimmer/trunk/delcher.h
===================================================================
--- trunk/packages/tigr-glimmer/trunk/delcher.h 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/delcher.h 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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 <stdio.h>
-#include <stdlib.h>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <math.h>
-#include <string.h>
-#include <ctype.h>
-#include <limits.h>
-#include <float.h>
-#include <time.h>
-#include <assert.h>
-#include <errno.h>
-#include <unistd.h>
-
-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 <class DT>
- DT Max (DT, DT);
-template <class DT>
- DT Min (DT, DT);
-template <class DT>
- void Swap (DT &, DT &);
-
-
-template <class DT>
-DT Max (DT A, DT B)
-
-// Return the larger of A and B .
-
- {
- if (A > B)
- return A;
- else
- return B;
- }
-
-
-
-template <class DT>
-DT Min (DT A, DT B)
-
-// Return the smaller of A and B .
-
- {
- if (A < B)
- return A;
- else
- return B;
- }
-
-
-
-template <class DT>
-void Swap (DT & A, DT & B)
-
-// Swap the values in A and B .
-
- {
- DT Save;
-
- Save = A;
- A = B;
- B = Save;
-
- return;
- }
-
-
-
-#endif
Deleted: trunk/packages/tigr-glimmer/trunk/run-glimmer2
===================================================================
--- trunk/packages/tigr-glimmer/trunk/run-glimmer2 2008-04-16 17:47:41 UTC (rev 1774)
+++ trunk/packages/tigr-glimmer/trunk/run-glimmer2 2008-04-16 20:15:57 UTC (rev 1775)
@@ -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.train >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
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