[med-svn] r1716 - in trunk/packages/tigr-glimmer/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Apr 9 04:28:51 UTC 2008
Author: charles-guest
Date: 2008-04-09 04:28:50 +0000 (Wed, 09 Apr 2008)
New Revision: 1716
Added:
trunk/packages/tigr-glimmer/trunk/debian/
trunk/packages/tigr-glimmer/trunk/debian/NEWS.Debian
trunk/packages/tigr-glimmer/trunk/debian/README.Debian
trunk/packages/tigr-glimmer/trunk/debian/changelog
trunk/packages/tigr-glimmer/trunk/debian/compat
trunk/packages/tigr-glimmer/trunk/debian/control
trunk/packages/tigr-glimmer/trunk/debian/copyright
trunk/packages/tigr-glimmer/trunk/debian/dirs
trunk/packages/tigr-glimmer/trunk/debian/docs
trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars
trunk/packages/tigr-glimmer/trunk/debian/index.html
trunk/packages/tigr-glimmer/trunk/debian/install
trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1
trunk/packages/tigr-glimmer/trunk/debian/manpages
trunk/packages/tigr-glimmer/trunk/debian/manpages.links
trunk/packages/tigr-glimmer/trunk/debian/rules
trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-anomaly.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-build-icm.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-extract.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer2.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-long-orfs.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer2.sgml
trunk/packages/tigr-glimmer/trunk/debian/watch
Modified:
trunk/packages/tigr-glimmer/trunk/Makefile
trunk/packages/tigr-glimmer/trunk/delcher.h
trunk/packages/tigr-glimmer/trunk/run-glimmer2
Log:
[svn-inject] Applying Debian modifications to trunk
Modified: trunk/packages/tigr-glimmer/trunk/Makefile
===================================================================
--- trunk/packages/tigr-glimmer/trunk/Makefile 2008-04-09 04:28:29 UTC (rev 1715)
+++ trunk/packages/tigr-glimmer/trunk/Makefile 2008-04-09 04:28:50 UTC (rev 1716)
@@ -9,11 +9,14 @@
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 *~
+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 = adjust anomaly build-icm check codon-usage compare-lists \
- extract generate get-len get-putative glimmer2 long-orfs
+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
@@ -25,43 +28,43 @@
all: $(ALL)
-adjust: adjust.o delcher.o
+tigr-adjust: adjust.o delcher.o
$(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
-anomaly: anomaly.o delcher.o gene.o
+tigr-anomaly: anomaly.o delcher.o gene.o
$(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
-build-icm: build-icm.o misc.o
+tigr-build-icm: build-icm.o misc.o
$(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
-check: check.o delcher.o
+tigr-check: check.o delcher.o
$(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
-codon-usage: codon-usage.o delcher.o gene.o
+tigr-codon-usage: codon-usage.o delcher.o gene.o
$(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
-compare-lists: compare-lists.o delcher.o
+tigr-compare-lists: compare-lists.o delcher.o
$(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
-extract: extract.o delcher.o
+tigr-extract: extract.o delcher.o
$(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
-generate: generate.o delcher.o gene.o
+tigr-generate: generate.o delcher.o gene.o
$(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
-get-len: get-len.o delcher.o
+tigr-get-len: get-len.o delcher.o
$(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
-get-putative: get-putative.o delcher.o
+tigr-get-putative: get-putative.o delcher.o
$(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
-glimmer2: glimmer2.o delcher.o gene.o rnabin.o
+tigr-glimmer2: glimmer2.o delcher.o gene.o rnabin.o
$(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
-long-orfs: long-orfs.o delcher.o gene.o
+tigr-long-orfs: long-orfs.o delcher.o gene.o
$(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
-rnabin: rnabin.o delcher.o
+tigr-rnabin: rnabin.o delcher.o
$(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
depend:
@@ -72,3 +75,349 @@
# 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
Property changes on: trunk/packages/tigr-glimmer/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/tigr-glimmer/trunk/debian/NEWS.Debian
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/NEWS.Debian (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/NEWS.Debian 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,5 @@
+With version 2.13-1, the binaries and man pages all have a prefix "tigr-"
+to avoid conflicts with other programs, with extract in particular.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 10 Nov 2004 17:33:46 +0100
+
Added: trunk/packages/tigr-glimmer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/README.Debian 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,15 @@
+tigr-glimmer for Debian
+-----------------------
+
+The glimmer software of the TIGR institute was renamed to tigr-glimmer
+because of a name conflict with the GNOME library. The package works
+for me, most efforts went into the reformatting of the readme files
+for the man pages, feedback is welcome.
+
+The upstream authors are very supportive of this debian package for
+their software and I thank them for this.
+
+With version 2.13-1, the binaries and man pages all have a prefix "tigr-"
+to avoid conflicts with other programs, with extract in particular.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 10 Nov 2004 12:33:46 +0100
Added: trunk/packages/tigr-glimmer/trunk/debian/changelog
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/changelog (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/changelog 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,21 @@
+tigr-glimmer (2.13-1.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Fix GCC 4.3 compatibility, patch by Kumar Appaiah (Closes: #461691)
+
+ -- Moritz Muehlenhoff <jmm at debian.org> Thu, 20 Mar 2008 00:02:06 +0100
+
+tigr-glimmer (2.13-1) unstable; urgency=low
+
+ * New upstream release - no significant changes for Linux users.
+ * Resolves conflict for "extract" binary and man page (Closes:Bug#227790,Bug#274780).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 10 Nov 2004 11:58:46 +0100
+
+tigr-glimmer (2.12-1) unstable; urgency=low
+
+ * Initial Release (Closes:#219453).
+ * Added man pages to upstream release
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 16 Oct 2003 17:33:46 +0200
+
Added: trunk/packages/tigr-glimmer/trunk/debian/compat
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/compat (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/compat 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1 @@
+4
Added: trunk/packages/tigr-glimmer/trunk/debian/control
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/control (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/control 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,20 @@
+Source: tigr-glimmer
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0), docbook-to-man, gzip, cdbs
+Standards-Version: 3.6.0
+
+Package: tigr-glimmer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: [Biology] Gene detection in archea and bacteria
+ Developed by the TIGR institute this software detects coding sequences in
+ bacteria and archea.
+ .
+ Glimmer is a system for finding genes in microbial DNA, especially the
+ genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
+ Markov Modeler) uses interpolated Markov models (IMMs) to identify the
+ coding regions and distinguish them from noncoding DNA.
+ .
+ Homepage: http://www.tigr.org/software/glimmer/
Added: trunk/packages/tigr-glimmer/trunk/debian/copyright
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/copyright (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/copyright 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,137 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Thu, 16 Oct 2003 17:33:46 +0200.
+
+It was downloaded from ftp://ftp.tigr.org/software/glimmer/
+
+Upstream Authors:
+ Art Delcher <adelcher at tigr.org>
+ Steven Salzberg <salzberg at tigr.org>
+
+Copyright:
+
+-=- Glimmer 2.1x COPYRIGHT NOTICE -=-
+
+Copyright (c) 1998-2003 by The Institute for Genomic
+Research (TIGR), Rockville, Maryland, U.S.A. All rights reserved.
+
+This software is OSI Certified Open Source Software. OSI Certified is a
+certification mark of the Open Source Initiative. Please refer to the
+'LICENSE' file for more information and the 'ACKNOWLEDGEMENTS' file for
+names of contributors to the code base.
+
+-=- GLIMMER 2.1x OPEN SOURCE LICENSE -=-
+
+The Artistic License
+
+Preamble
+
+The intent of this document is to state the conditions under which a
+Package may be copied, such that the Copyright Holder maintains some
+semblance of artistic control over the development of the package,
+while giving the users of the package the right to use and distribute
+the Package in a more-or-less customary fashion, plus the right to
+make reasonable modifications.
+
+Definitions:
+ * "Package" refers to the collection of files distributed by the
+ Copyright Holder, and derivatives of that collection of files
+ created through textual modification.
+ * "Standard Version" refers to such a Package if it has not been
+ modified, or has been modified in accordance with the wishes of
+ the Copyright Holder.
+ * "Copyright Holder" is whoever is named in the copyright or
+ copyrights for the package.
+ * "You" is you, if you're thinking about copying or distributing
+ this Package.
+ * "Reasonable copying fee" is whatever you can justify on the
+ basis of media cost, duplication charges, time of people
+ involved, and so on. (You will not be required to justify it to
+ the Copyright Holder, but only to the computing community at
+ large as a market that must bear the fee.)
+ * "Freely Available" means that no fee is charged for the item
+ itself, though there may be fees involved in handling the
+ item. It also means that recipients of the item may redistribute
+ it under the same conditions they received it.
+
+1. You may make and give away verbatim copies of the source form of
+ the Standard Version of this Package without restriction, provided
+ that you duplicate all of the original copyright notices and
+ associated disclaimers.
+
+2. You may apply bug fixes, portability fixes and other modifications
+ derived from the Public Domain or from the Copyright Holder. A
+ Package modified in such a way shall still be considered the
+ Standard Version.
+
+3. You may otherwise modify your copy of this Package in any way,
+ provided that you insert a prominent notice in each changed file
+ stating how and when you changed that file, and provided that you
+ do at least ONE of the following:
+
+ a) place your modifications in the Public Domain or otherwise make
+ them Freely Available, such as by posting said modifications to
+ Usenet or an equivalent medium, or placing the modifications on a
+ major archive site such as ftp.uu.net, or by allowing the
+ Copyright Holder to include your modifications in the Standard
+ Version of the Package.
+
+ b) use the modified Package only within your corporation or
+ organization.
+
+ c) rename any non-standard executables so the names do not
+ conflict with standard executables, which must also be provided,
+ and provide a separate manual page for each non-standard
+ executable that clearly documents how it differs from the Standard
+ Version.
+
+ d) make other distribution arrangements with the Copyright Holder.
+
+4. You may distribute the programs of this Package in object code or
+ executable form, provided that you do at least ONE of the
+ following:
+
+ a) distribute a Standard Version of the executables and library
+ files, together with instructions (in the manual page or
+ equivalent) on where to get the Standard Version.
+
+ b) accompany the distribution with the machine-readable source of
+ the Package with your modifications.
+
+ c) accompany any non-standard executables with their corresponding
+ Standard Version executables, giving the non-standard executables
+ non-standard names, and clearly documenting the differences in
+ manual pages (or equivalent), together with instructions on where
+ to get the Standard Version.
+
+ d) make other distribution arrangements with the Copyright Holder.
+
+5. You may charge a reasonable copying fee for any distribution of
+ this Package. You may charge any fee you choose for support of this
+ Package. You may not charge a fee for this Package itself. However,
+ you may distribute this Package in aggregate with other (possibly
+ commercial) programs as part of a larger (possibly commercial)
+ software distribution provided that you do not advertise this
+ Package as a product of your own.
+
+6. The scripts and library files supplied as input to or produced as
+ output from the programs of this Package do not automatically fall
+ under the copyright of this Package, but belong to whomever
+ generated them, and may be sold commercially, and may be aggregated
+ with this Package.
+
+7. C or perl subroutines supplied by you and linked into this Package
+ shall not be considered part of this Package.
+
+8. The name of the Copyright Holder may not be used to endorse or
+ promote products derived from this software without specific prior
+ written permission.
+
+9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+The End
+This license is approved by the Open Source Initiative
+(www.opensource.org) for certifying software as OSI Certified Open
+Source.
+
Added: trunk/packages/tigr-glimmer/trunk/debian/dirs
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/dirs (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/dirs 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/tigr-glimmer/trunk/debian/docs
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/docs (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/docs 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,7 @@
+README
+ACKNOWLEDGEMENTS
+changelog.gz
+build-icm.readme
+extract.readme
+glimmer2.readme
+long-orfs.readme
Added: trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1 @@
+shlibs:Depends=libc6 (>= 2.3.2-1), libgcc1 (>= 1:3.3.1-1), libstdc++5 (>= 1:3.3.1-1)
Added: trunk/packages/tigr-glimmer/trunk/debian/index.html
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/index.html (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/index.html 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<HTML
+><HEAD
+><TITLE
+>EXTRACT</TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"></HEAD
+><BODY
+CLASS="REFENTRY"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><H1
+><A
+NAME="AEN1"
+></A
+>EXTRACT</H1
+><DIV
+CLASS="REFNAMEDIV"
+><A
+NAME="AEN15"
+></A
+><H2
+>Name</H2
+>extract -- Fine start/stop positions of genes in genome sequence</DIV
+><DIV
+CLASS="REFSYNOPSISDIV"
+><A
+NAME="AEN18"
+></A
+><H2
+>Synopsis</H2
+><P
+><B
+CLASS="COMMAND"
+>long-orgs</B
+> [genome-file <VAR
+CLASS="OPTION"
+><VAR
+CLASS="REPLACEABLE"
+>options</VAR
+></VAR
+>]</P
+></DIV
+><DIV
+CLASS="REFSECT1"
+><A
+NAME="AEN24"
+></A
+><H2
+>DESCRIPTION</H2
+><P
+>Program extract takes a FASTA format sequence file and a file
+with a list of start/stop positions in that file (e.g., as produced
+by the long-orfs program) and extracts and outputs the
+specified sequences.</P
+><P
+>The first command-line argument is the name of the sequence file,
+which must be in FASTA format.</P
+><P
+>The second command-line argument is the name of the coordinate file.
+It must contain a list of pairs of positions in the first file, one
+per line. The format of each entry is:</P
+><P
+> <IDstring>> <start position> <stop position></P
+><P
+>This file should contain no other information, so if you're using
+the output of glimmer or long-orfs , you'll have to cut off
+header lines.</P
+><P
+>The output of the program goes to the standard output and has one
+line for each line in the coordinate file. Each line contains
+the IDstring , followed by white space, followed by the substring
+of the sequence file specified by the coordinate pair. Specifically,
+the substring starts at the first position of the pair and ends at
+the second position (inclusive). If the first position is bigger
+than the second, then the DNA reverse complement of each position
+is generated. Start/stop pairs that "wrap around" the end of the
+genome are allowed.</P
+></DIV
+><DIV
+CLASS="REFSECT1"
+><A
+NAME="AEN32"
+></A
+><H2
+>OPTIONS</H2
+><P
+></P
+><DIV
+CLASS="VARIABLELIST"
+><DL
+><DT
+><VAR
+CLASS="OPTION"
+>-skip</VAR
+></DT
+><DD
+><P
+> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</P
+></DD
+><DT
+><VAR
+CLASS="OPTION"
+>-l</VAR
+></DT
+><DD
+><P
+> makes the output omit an sequences shorter than n characters.
+ n includes the 3 skipped characters if the -skip switch
+ is one.
+ </P
+></DD
+></DL
+></DIV
+></DIV
+><DIV
+CLASS="REFSECT1"
+><A
+NAME="AEN45"
+></A
+><H2
+>SEE ALSO</H2
+><P
+>glimmer2 (1),
+long-orfs (1),
+adjust (1),
+anomaly (1),
+build-icm (1),
+check (1),
+codon-usage (1),
+compare-lists (1),
+extract (1),
+generate (1),
+get-len (1),
+get-putative (1),</P
+><P
+>http://www.tigr.org/software/glimmer/</P
+><P
+>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</P
+></DIV
+><DIV
+CLASS="REFSECT1"
+><A
+NAME="AEN50"
+></A
+><H2
+>AUTHOR</H2
+><P
+>This manual page was quickly copied from the glimmer web site by Steffen Moeller <CODE
+CLASS="EMAIL"
+><<A
+HREF="mailto:moeller at pzr.uni-rostock.de"
+>moeller at pzr.uni-rostock.de</A
+>></CODE
+> for
+ the <SPAN
+CLASS="PRODUCTNAME"
+>Debian</SPAN
+> system.
+ </P
+></DIV
+></BODY
+></HTML
+>
\ No newline at end of file
Added: trunk/packages/tigr-glimmer/trunk/debian/install
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/install (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,13 @@
+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
Added: trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1 (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,190 @@
+...\" $Header: /aolnet/dev/src/CVS/sgml/docbook-to-man/cmd/docbook-to-man.sh,v 1.1.1.1 1998/11/13 21:31:59 db3l Exp $
+...\"
+...\" transcript compatibility for postscript use.
+...\"
+...\" synopsis: .P! <file.ps>
+...\"
+.de P!
+.fl
+\!!1 setgray
+.fl
+\\&.\"
+.fl
+\!!0 setgray
+.fl \" force out current output buffer
+\!!save /psv exch def currentpoint translate 0 0 moveto
+\!!/showpage{}def
+.fl \" prolog
+.sy sed -e 's/^/!/' \\$1\" bring in postscript file
+\!!psv restore
+.
+.de pF
+.ie \\*(f1 .ds f1 \\n(.f
+.el .ie \\*(f2 .ds f2 \\n(.f
+.el .ie \\*(f3 .ds f3 \\n(.f
+.el .ie \\*(f4 .ds f4 \\n(.f
+.el .tm ? font overflow
+.ft \\$1
+..
+.de fP
+.ie !\\*(f4 \{\
+. ft \\*(f4
+. ds f4\"
+' br \}
+.el .ie !\\*(f3 \{\
+. ft \\*(f3
+. ds f3\"
+' br \}
+.el .ie !\\*(f2 \{\
+. ft \\*(f2
+. ds f2\"
+' br \}
+.el .ie !\\*(f1 \{\
+. ft \\*(f1
+. ds f1\"
+' br \}
+.el .tm ? font underflow
+..
+.ds f1\"
+.ds f2\"
+.ds f3\"
+.ds f4\"
+'\" t
+.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
+.TH "LONG-ORFS" "1"
+.SH "NAME"
+long-orfs \(em Find/Score potential genes in genome-file using
+the probability model in icm-file
+.SH "SYNOPSIS"
+.PP
+\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
+.SH "DESCRIPTION"
+.PP
+Program long-orfs takes a sequence file (in FASTA format) and
+outputs a list of all long "potential genes" in it that do not
+overlap by too much. By "potential gene" I mean the portion of
+an orf from the first start codon to the stop codon at the end.
+.PP
+The first few lines of output specify the settings of various
+parameters in the program:
+.PP
+Minimum gene length is the length of the smallest fragment
+considered to be a gene. The length is measured from the first base
+of the start codon to the last base *before* the stop codon.
+This value can be specified when running the program with the -g option.
+By default, the program now (April 2003) will compute an optimal length
+for this parameter, where "optimal" is the value that produces the
+greatest number of long ORFs, thereby increasing the amount of data
+used for training.
+.PP
+Minimum overlap length is a lower bound on the number of bases overlap
+between 2 genes that is considered a problem. Overlaps shorter than
+this are ignored.
+.PP
+Minimum overlap percent is another lower bound on the number of bases
+overlap that is considered a problem. Overlaps shorter than this
+percentage of *both* genes are ignored.
+.PP
+The next portion of the output is a list of potential genes:
+.PP
+Column 1 is an ID number for reference purposes. It is assigned
+sequentially starting with 1 to all long potential genes. If
+overlapping genes are eliminated, gaps in the numbers will occur.
+The ID prefix is specified in the constant ID_PREFIX .
+.PP
+Column 2 is the position of the first base of the first start codon in
+the orf. Currently I use atg, and gtg as start codons. This is
+easily changed in the function Is_Start () .
+.PP
+Column 3 is the position of the last base *before* the stop codon. Stop
+codons are taa, tag, and tga. Note that for orfs in the reverse
+reading frames have their start position higher than the end position.
+The order in which orfs are listed is in increasing order by
+Max {OrfStart, End}, i.e., the highest numbered position in the orf,
+except for orfs that "wrap around" the end of the sequence.
+.PP
+When two genes with ID numbers overlap by at least a sufficient
+amount (as determined by Min_Olap and Min_Olap_Percent ), they
+are eliminated and do not appear in the output.
+.PP
+The final output of the program (sent to the standard error file so
+it does not show up when output is redirected to a file) is the
+length of the longest orf found.
+.PP
+
+Specifying Different Start and Stop Codons:
+.PP
+To specify different sets of start and stop codons, modify the file
+gene.h . Specifically, the functions:
+.PP
+Is_Forward_Start Is_Reverse_Start Is_Start
+Is_Forward_Stop Is_Reverse_Stop Is_Stop
+.PP
+are used to determine what is used for start and stop codons.
+.PP
+Is_Start and Is_Stop do simple string comparisons to specify
+which patterns are used. To add a new pattern, just add the comparison
+for it. To remove a pattern, comment out or delete the comparison
+for it.
+.PP
+The other four functions use a bit comparison to determine start and
+stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
+for each base, one bit for each possible value of the bases, T, G, C
+or A. Thus the bit pattern 0010 0101 1100 represents the base
+pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
+comparisons, more complicated patterns involving ambiguous reads
+can be tested efficiently. Simple patterns can be tested as in
+the current code.
+.PP
+For example, to insert an additional start codon of CAT requires 3 changes:
+1. The line
+|| (Codon & 0x218) == Codon
+should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
+represents CAT.
+2. The line
+|| (Codon & 0x184) == Codon
+should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
+represents ATG, which is the reverse-complement of CAT. Alternately,
+the #define constant ATG_MASK could be used.
+3. The line
+|| strncmp (S, "cat", 3) == 0
+should be inserted into Is_Start .
+.SH "OPTIONS"
+.IP "\fB-g \fIn\fR\fP" 10
+Set minimum gene length to n. Default is to compute an
+optimal value automatically. Don't change this unless you
+know what you're doing.
+.IP "\fB-l\fP" 10
+Regard the genome as linear (not circular), i.e., do not allow
+genes to "wrap around" the end of the genome.
+This option works on both glimmer and long-orfs .
+The default behavior is to regard the genome as circular.
+.IP "\fB-o \fIn\fR\fP" 10
+Set maximum overlap length to n. Overlaps shorter than this
+are permitted. (Default is 0 bp.)
+.IP "\fB-p \fIn\fR\fP" 10
+Set maximum overlap percentage to n%. Overlaps shorter than
+this percentage of *both* strings are ignored. (Default is 10%.)
+.SH "SEE ALSO"
+.PP
+glimmer2 (1),
+adjust (1),
+anomaly (1),
+build-icm (1),
+check (1),
+codon-usage (1),
+compare-lists (1),
+extract (1),
+generate (1),
+get-len (1),
+get-putative (1),
+.PP
+http://www.tigr.org/software/glimmer/
+.PP
+Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.
+.SH "AUTHOR"
+.PP
+This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller at pzr.uni-rostock.de for
+the \fBDebian\fP system.
+
+...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43
Added: trunk/packages/tigr-glimmer/trunk/debian/manpages
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/manpages (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/manpages 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,13 @@
+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-glimmer2.1
+debian/tigr-long-orfs.1
+debian/tigr-run-glimmer2.1
Added: trunk/packages/tigr-glimmer/trunk/debian/manpages.links
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/manpages.links (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/manpages.links 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1 @@
+tigr-glimmer glimmer2
Added: trunk/packages/tigr-glimmer/trunk/debian/rules
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/rules (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/rules 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,58 @@
+#!/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
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+.PHONY: clean
+
+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
+
+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
+
+.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
Property changes on: trunk/packages/tigr-glimmer/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,119 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>Novermber 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+the program lacks a description
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-adjust</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+tigr-long-orfs (1)
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-anomaly.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-anomaly.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-anomaly.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,124 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+The program lacks a description
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-anomaly</command>
+ <arg>>dna-file</arg>
+ <arg>>coord-file</arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-build-icm.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-build-icm.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-build-icm.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,162 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>Novemver 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER<title>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Ceates and outputs an interpolated Markov model(IMM)</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-build-icm</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+Program build-icm.c creates and outputs an interpolated Markov
+model (IMM) as described in the paper
+ A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
+ Improved Microbial Gene Identification with Glimmer.
+ Nucleic Acids Research, 1999, in press.
+Please reference this paper if you use the system as part of any
+published research.
+</para><para>
+Input comes from the file named on the command-line. Format should be
+one string per line. Each line has an ID string followed by white space
+followed by the sequence itself. The script run-glimmer2 generates
+an input file in the correct format using the 'extract' program.
+</para><para>
+The IMM is constructed as follows: For a given context, say
+acgtta, we want to estimate the probability distribution of the
+next character. We shall do this as a linear combination of the
+observed probability distributions for this context and all of
+its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. By
+observed distributions I mean the counts of the number of
+occurrences of these strings in the training set. The linear
+combination is determined by a set of probabilities, lambda, one
+for each context string. For context acgtta the linear combination
+coefficients are:
+</para><para>
+ lambda (acgtta)
+ (1 - lambda (acgtta)) x lambda (cgtta)
+ (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta)
+ (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta)
+ (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta))
+ x (1 - lambda (tta)) x (1 - lambda (ta)) x (1 - lambda (a))
+</para><para>
+We compute the lambda values for each context as follows:
+ - If the number of observations in the training set is >= the constant
+ SAMPLE_SIZE_BOUND, the lambda for that context is 1.0
+ - Otherwise, do a chi-square test on the observations for this context
+ compared to the distribution predicted for the one-character shorter
+ suffix context.
+ If the chi-square significance < 0.5, set the lambda for this context to 0.0
+ Otherwise set the lambda for this context to:
+ (chi-square significance) x (# observations) / SAMPLE_WEIGHT
+</para><para>
+To run the program:
+</para><para>
+ build-icm <train.seq > train.model
+</para><para>
+ This will use the training data in train.seq to produce the file
+ train.model, containing your IMM.
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-long-orfs (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-extract (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+ </para>
+ <para>http://www.tigr.org/software/glimmer/</para>
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site and readme file by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,118 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+The program lacks a description.
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-check</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,122 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+The program lacks a description
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-codon-usage</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,122 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+unknown
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-compare-lists</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-extract.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-extract.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-extract.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,165 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+Fine start/stop positions of genes in genome sequence
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-extract</command>
+ <arg>genome-file <option><replaceable>options</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+Program extract takes a FASTA format sequence file and a file
+with a list of start/stop positions in that file (e.g., as produced
+by the long-orfs program) and extracts and outputs the
+specified sequences.
+</para><para>
+The first command-line argument is the name of the sequence file,
+which must be in FASTA format.
+</para><para>
+The second command-line argument is the name of the coordinate file.
+It must contain a list of pairs of positions in the first file, one
+per line. The format of each entry is:
+</para><para> <IDstring>> <start position> <stop position>
+</para><para>This file should contain no other information, so if you're using
+the output of glimmer or long-orfs , you'll have to cut off
+header lines.
+</para><para>
+The output of the program goes to the standard output and has one
+line for each line in the coordinate file. Each line contains
+the IDstring , followed by white space, followed by the substring
+of the sequence file specified by the coordinate pair. Specifically,
+the substring starts at the first position of the pair and ends at
+the second position (inclusive). If the first position is bigger
+than the second, then the DNA reverse complement of each position
+is generated. Start/stop pairs that "wrap around" the end of the
+genome are allowed.
+</para>
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-skip</option></term>
+ <listitem>
+ <para> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-l</option></term><listitem><para>
+ makes the output omit an sequences shorter than n characters.
+ n includes the 3 skipped characters if the -skip switch
+ is one.
+ </para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-long-orfs (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,118 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+This program lacks a description.
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-generate</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,118 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+This program lacks a description.
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-get-len</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,114 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>
+ </refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-get-putative</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+tigr-long-orfs (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer2.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer2.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer2.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,246 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>
+Find/Score potential genes in genome-file using the probability model in icm-file
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-glimmer2</command>
+ <arg><option><replaceable>genome-file</replaceable></option></arg>
+ <arg><option><replaceable>icm-file</replaceable></option></arg>
+ <arg><option><replaceable>[options]</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+<command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
+</para><para>
+<command>&dhpackage;</command> is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site.
+</para><para>
+A special version of <command>&dhpackage;</command> designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system.
+</para><para>
+The <command>&dhpackage;</command> system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. <command>&dhpackage;</command> automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far.
+ <command>&dhpackage;</command> is a program that...</para>
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-C <replaceable>n</replaceable></option></term>
+ <listitem>
+ <para>Use n as GC percentage of independent model</para>
+ <para>Note: n should be a percentage, e.g., -C 45.2</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
+ </varlistentry>
+ <varlistentry>
+<term><option>-i <replaceable>filename</replaceable></option></term>
+ <listitem>
+ <para>Use <option><replaceable>filename</replaceable></option>
+ to select regions of bases that are off
+ limits, so that no bases within that area will be examined
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-l</option></term>
+ <listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-L <replaceable>filename</replaceable></option></term>
+ <listitem><para>Use filename to specify a list of orfs that should
+ be scored separately, with no overlap rules
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-M</option></term>
+ <listitem><para>Input is a multifasta file of separate genes to be scored
+ separately, with no overlap rules
+ </para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-o <replaceable>n</replaceable></option></term>
+ <listitem>
+ <para>Set minimum overlap length to n. Overlaps shorter than this
+ are ignored.
+ </para></listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-p <replaceable>n</replaceable></option></term>
+ <listitem>
+ <para>
+ Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored.
+ </para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-q <replaceable>n</replaceable></option></term>
+ <listitem>
+ <para>Set the maximum length orf that can be rejected because of
+ the independent probability score column to (n - 1)
+ </para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-r</option></term>
+ <listitem>
+ <para>
+ Don't use independent probability score column
+ </para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>+r</option></term>
+ <listitem><para>
+Use independent probability score column
+ </para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-r</option></term>
+ <listitem>
+ <para>
+ Don't use independent probability score column
+ </para> </listitem> </varlistentry> <varlistentry>
+ <term><option>-s <replaceable>s</replaceable></option></term>
+ <listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
+ </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>+S</option></term>
+ <listitem>
+ <para>
+ Do use stricter independent intergenic model that doesn't
+ give probabilities to in-frame stop codons. (Option is obsolete
+ since this is now the only behaviour
+ </para> </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-t <replaceable>n</replaceable></option></term>
+ <listitem><para>
+ Set threshold score for calling as gene to n. If the in-frame
+ score >= n, then the region is given a number and considered
+ a potential gene.
+ </para> </listitem>
+</varlistentry>
+<varlistentry>
+ <term><option>-w <replaceable>n</replaceable> </option></term>
+ <listitem><para>
+ Use "weak" scores on tentative genes n or longer. Weak
+ scores ignore the independent probability score.
+ </para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+tigr-glimmer2 (1),
+tigr-long-orfs (1)
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+ <para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-long-orfs.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-long-orfs.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-long-orfs.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,238 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>LONG-ORFS</refentrytitle>">
+ <!ENTITY dhpackage "long-orfs">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+Find/Score potential genes in genome-file using
+the probability model in icm-file
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-long-orgs</command>
+ <arg>genome-file <option><replaceable>options</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+Program long-orfs takes a sequence file (in FASTA format) and
+outputs a list of all long "potential genes" in it that do not
+overlap by too much. By "potential gene" I mean the portion of
+an orf from the first start codon to the stop codon at the end.
+</para><para>
+The first few lines of output specify the settings of various
+parameters in the program:
+</para><para>
+ Minimum gene length is the length of the smallest fragment
+ considered to be a gene. The length is measured from the first base
+ of the start codon to the last base *before* the stop codon.
+ This value can be specified when running the program with the -g option.
+ By default, the program now (April 2003) will compute an optimal length
+ for this parameter, where "optimal" is the value that produces the
+ greatest number of long ORFs, thereby increasing the amount of data
+ used for training.
+</para><para>
+ Minimum overlap length is a lower bound on the number of bases overlap
+ between 2 genes that is considered a problem. Overlaps shorter than
+ this are ignored.
+</para><para>
+ Minimum overlap percent is another lower bound on the number of bases
+ overlap that is considered a problem. Overlaps shorter than this
+ percentage of *both* genes are ignored.
+</para><para>
+The next portion of the output is a list of potential genes:
+</para><para>
+ Column 1 is an ID number for reference purposes. It is assigned
+ sequentially starting with 1 to all long potential genes. If
+ overlapping genes are eliminated, gaps in the numbers will occur.
+ The ID prefix is specified in the constant ID_PREFIX .
+</para><para>
+ Column 2 is the position of the first base of the first start codon in
+ the orf. Currently I use atg, and gtg as start codons. This is
+ easily changed in the function Is_Start () .
+</para><para>
+ Column 3 is the position of the last base *before* the stop codon. Stop
+ codons are taa, tag, and tga. Note that for orfs in the reverse
+ reading frames have their start position higher than the end position.
+ The order in which orfs are listed is in increasing order by
+ Max {OrfStart, End}, i.e., the highest numbered position in the orf,
+ except for orfs that "wrap around" the end of the sequence.
+</para><para>
+When two genes with ID numbers overlap by at least a sufficient
+amount (as determined by Min_Olap and Min_Olap_Percent ), they
+are eliminated and do not appear in the output.
+</para><para>
+The final output of the program (sent to the standard error file so
+it does not show up when output is redirected to a file) is the
+length of the longest orf found.
+</para><para>
+
+
+Specifying Different Start and Stop Codons:
+</para><para>
+To specify different sets of start and stop codons, modify the file
+gene.h . Specifically, the functions:
+</para><para>
+ Is_Forward_Start Is_Reverse_Start Is_Start
+ Is_Forward_Stop Is_Reverse_Stop Is_Stop
+</para><para>
+are used to determine what is used for start and stop codons.
+</para><para>
+Is_Start and Is_Stop do simple string comparisons to specify
+which patterns are used. To add a new pattern, just add the comparison
+for it. To remove a pattern, comment out or delete the comparison
+for it.
+</para><para>
+The other four functions use a bit comparison to determine start and
+stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
+for each base, one bit for each possible value of the bases, T, G, C
+or A. Thus the bit pattern 0010 0101 1100 represents the base
+pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
+comparisons, more complicated patterns involving ambiguous reads
+can be tested efficiently. Simple patterns can be tested as in
+the current code.
+</para><para>
+For example, to insert an additional start codon of CAT requires 3 changes:
+1. The line
+ || (Codon & 0x218) == Codon
+ should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
+ represents CAT.
+2. The line
+ || (Codon & 0x184) == Codon
+ should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
+ represents ATG, which is the reverse-complement of CAT. Alternately,
+ the #define constant ATG_MASK could be used.
+3. The line
+ || strncmp (S, "cat", 3) == 0
+ should be inserted into Is_Start .
+</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-g <replaceable>n</replaceable></option></term>
+ <listitem>
+ <para> Set minimum gene length to n. Default is to compute an
+ optimal value automatically. Don't change this unless you
+ know what you're doing.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-l</option></term><listitem><para>Regard the genome as linear (not circular), i.e., do not allow
+ genes to "wrap around" the end of the genome.
+ This option works on both glimmer and long-orfs .
+ The default behavior is to regard the genome as circular.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-o <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap length to n. Overlaps shorter than this
+ are permitted. (Default is 0 bp.)</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-p <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap percentage to n%. Overlaps shorter than
+ this percentage of *both* strings are ignored. (Default is 10%.)</para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer2.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer2.sgml (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer2.sgml 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,120 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 10, 2004</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
+ <!ENTITY dhpackage "tigr-glimmer">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>
+Apply the suite of programs within glimmer2 to a a prokaryotic or archean genome.
+</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>tigr-run-glimmer2</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+<para>
+A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
+</para>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+tigr-glimmer2 (1),
+tigr-adjust (1),
+tigr-anomaly (1),
+tigr-build-icm (1),
+tigr-check (1),
+tigr-codon-usage (1),
+tigr-compare-lists (1),
+tigr-extract (1),
+tigr-generate (1),
+tigr-get-len (1),
+tigr-get-putative (1),
+tigr-long-orfs (1),
+</para>
+<para>
+http://www.tigr.org/software/glimmer/
+</para>
+
+ <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
+ the &debian; system.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
Added: trunk/packages/tigr-glimmer/trunk/debian/watch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/watch (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/watch 2008-04-09 04:28:50 UTC (rev 1716)
@@ -0,0 +1,5 @@
+# format version number, currently 2; this line is compulsory!
+version=2
+
+# This is one format for an HTTP site, which is the same as the FTP format
+ftp://ftp.tigr.org/pub/software/Glimmer/glimmer(\d+).tar.gz
Modified: trunk/packages/tigr-glimmer/trunk/delcher.h
===================================================================
--- trunk/packages/tigr-glimmer/trunk/delcher.h 2008-04-09 04:28:29 UTC (rev 1715)
+++ trunk/packages/tigr-glimmer/trunk/delcher.h 2008-04-09 04:28:50 UTC (rev 1716)
@@ -18,9 +18,9 @@
#include <stdio.h>
#include <stdlib.h>
-#include <iostream.h>
-#include <iomanip.h>
-#include <fstream.h>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
#include <math.h>
#include <string.h>
#include <ctype.h>
@@ -31,6 +31,7 @@
#include <errno.h>
#include <unistd.h>
+using namespace std;
#define TRUE 1
#define FALSE 0
Modified: trunk/packages/tigr-glimmer/trunk/run-glimmer2
===================================================================
--- trunk/packages/tigr-glimmer/trunk/run-glimmer2 2008-04-09 04:28:29 UTC (rev 1715)
+++ trunk/packages/tigr-glimmer/trunk/run-glimmer2 2008-04-09 04:28:50 UTC (rev 1716)
@@ -1,3 +1,4 @@
+#!/bin/sh
echo "run Glimmer2"
clear
echo "Genome is " $1
@@ -3,13 +4,13 @@
echo "Find non-overlapping orfs in tmp.coord"
rm -f tmp.coord
-long-orfs $1 | get-putative >tmp.coord
+tigr-long-orfs $1 | tigr-get-putative >tmp.coord
echo "Extract training sequences to tmp.train"
rm -f tmp.train
-extract $1 tmp.coord >tmp.train
+tigr-extract $1 tmp.coord >tmp.train
wc tmp.train
echo "Build interpolated context model in tmp.model"
rm -f tmp.model
-build-icm <tmp.train >tmp.model
+tigr-build-icm <tmp.train >tmp.model
echo "Predict genes with Glimmer2 with coordinates in g2.coord"
rm -f g2.coord
-glimmer2 $1 tmp.model | get-putative >g2.coord
+tigr-glimmer2 $1 tmp.model | tigr-get-putative >g2.coord
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