[med-svn] r15193 - in trunk/packages/glam2: . branches branches/meme branches/meme/debian branches/meme/debian/debian-compile branches/meme/debian/debian-docs branches/meme/debian/debian-examples branches/meme/debian/glam2_manpages branches/meme/debian/patches branches/meme/debian/source
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 21:53:31 UTC 2013
Author: tille
Date: 2013-11-20 21:53:31 +0000 (Wed, 20 Nov 2013)
New Revision: 15193
Added:
trunk/packages/glam2/branches/
trunk/packages/glam2/branches/meme/
trunk/packages/glam2/branches/meme/debian/
trunk/packages/glam2/branches/meme/debian/README.Debian
trunk/packages/glam2/branches/meme/debian/README.source
trunk/packages/glam2/branches/meme/debian/changelog
trunk/packages/glam2/branches/meme/debian/compat
trunk/packages/glam2/branches/meme/debian/control
trunk/packages/glam2/branches/meme/debian/copyright
trunk/packages/glam2/branches/meme/debian/debian-compile/
trunk/packages/glam2/branches/meme/debian/debian-compile/Makefile
trunk/packages/glam2/branches/meme/debian/debian-compile/config.h
trunk/packages/glam2/branches/meme/debian/debian-compile/dir.h
trunk/packages/glam2/branches/meme/debian/debian-compile/glam2_convolve.c
trunk/packages/glam2/branches/meme/debian/debian-docs/
trunk/packages/glam2/branches/meme/debian/debian-docs/index.html
trunk/packages/glam2/branches/meme/debian/debian-examples/
trunk/packages/glam2/branches/meme/debian/debian-examples/crp0.s
trunk/packages/glam2/branches/meme/debian/debian-examples/dna.alph
trunk/packages/glam2/branches/meme/debian/debian-examples/glam_tfbs.1comp
trunk/packages/glam2/branches/meme/debian/debian-examples/lipocalin.s
trunk/packages/glam2/branches/meme/debian/debian-examples/recode3.20comp
trunk/packages/glam2/branches/meme/debian/debian-examples/robinson.alph
trunk/packages/glam2/branches/meme/debian/docs
trunk/packages/glam2/branches/meme/debian/examples
trunk/packages/glam2/branches/meme/debian/glam2.doc-base.manual
trunk/packages/glam2/branches/meme/debian/glam2.doc-base.method
trunk/packages/glam2/branches/meme/debian/glam2_manpages/
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2-purge.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2fft.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2format.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2html.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2mask.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2psfm.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan.1
trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan2html.1
trunk/packages/glam2/branches/meme/debian/install
trunk/packages/glam2/branches/meme/debian/manpages
trunk/packages/glam2/branches/meme/debian/patches/
trunk/packages/glam2/branches/meme/debian/patches/fix_fftw3_build.patch
trunk/packages/glam2/branches/meme/debian/patches/series
trunk/packages/glam2/branches/meme/debian/rules
trunk/packages/glam2/branches/meme/debian/source/
trunk/packages/glam2/branches/meme/debian/source/format
trunk/packages/glam2/branches/meme/debian/upstream
trunk/packages/glam2/branches/meme/debian/watch
Log:
Add branch for glam2 obtained from meme source
Added: trunk/packages/glam2/branches/meme/debian/README.Debian
===================================================================
--- trunk/packages/glam2/branches/meme/debian/README.Debian (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/README.Debian 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,9 @@
+glam2 for Debian
+----------------
+
+We renamed purge glam2-purge, to avoid namespace collision.
+
+glam2 is compiled with -O2 optimisation level. Please contact us if you notice
+performance issues compared to -O3.
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 13 Nov 2007 00:35:50 +0100
Added: trunk/packages/glam2/branches/meme/debian/README.source
===================================================================
--- trunk/packages/glam2/branches/meme/debian/README.source (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/README.source 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,36 @@
+Formerly glam2 was a seprate project at
+http://bioinformatics.org.au/glam2/ but was now merged with the MEME
+project (see http://acb.qfab.org/acb/glam2/). Unfortunately the MEME
+license is not DFSG free but the authors have given permission to
+extract the successor code of glam2 under the old license of this
+code. This is realised via uscan by excluding all the files mentioned
+in Files-Excluded inside debian/copyright.
+
+iHowever, the following files are taken needed from main MEME and do not
+belong to the formerly separate glam2 source:
+
+ alphabet.[ch]
+ array.[ch]
+ array-list.[ch]
+ binary-search.[ch]
+ ceqlogo.[ch]
+ eps2png.[ch]
+ hash_alph.h
+ io.[ch]
+ macros.h
+ matrix.[ch]
+ motif.[ch]
+ motif-in-flags.h
+ motif-in.h
+ motif-spec.h
+ red-black-tree.[ch]
+ regex-utils.[ch]
+ string-builder.[ch]
+ string-list.h
+ user.h
+ utils.[ch]
+
+It has to be clarified with upstream whether also these files could be
+relicensed under a free license.
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Nov 2013 15:17:01 +0100
Added: trunk/packages/glam2/branches/meme/debian/changelog
===================================================================
--- trunk/packages/glam2/branches/meme/debian/changelog (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/changelog 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,55 @@
+glam2 (1:4.9.1+dfsg-1) UNRELEASED; urgency=low
+
+ * New upstream version integrated into MEME
+
+ [ Charles Plessy ]
+ * Documented information in ‘debian/upstream’.
+
+ [ Andreas Tille ]
+ * debian/upstream: Took over some bit sof information from tasks
+ file and move DOI+PMID to references
+ * debian/control:
+ - Fixed Vcs fields
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debian/source/format: 3.0 (quilt)
+ * debhelper 9 (control+compat)
+ * Moved manpages to debian/glam2_manpages
+ * debian/rules: cdbs -> dh
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Nov 2013 15:17:01 +0100
+
+glam2 (1064-2) unstable; urgency=low
+
+ * debian/control, debian/reference: simplified long description and moved
+ bibliographic references to a new file.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 21 Apr 2009 21:49:54 +0900
+
+glam2 (1064-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release
+ - One paragraph added to the tutorial.
+ - Uses CFLAGS in makefiles (thanks Martin!)
+ * Changed the doc-base section according to the new policy.
+ * Updated my email address.
+ * Added a get-orig-source target in debian/rules.
+ * debian/patches/Makefiles removed because obsoleted.
+
+ [ Andreas Tille ]
+ * Better formatting of long description.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 19 May 2008 18:46:20 +0900
+
+glam2 (1058-1) unstable; urgency=low
+
+ * New upstream release (Fixes bug in usage message: z_def was out of order.)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 14 Feb 2008 13:05:54 +0900
+
+glam2 (1056-1) unstable; urgency=low
+
+ * Initial release (Closes: #45237)
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 13 Nov 2007 00:35:50 +0100
+
Added: trunk/packages/glam2/branches/meme/debian/compat
===================================================================
--- trunk/packages/glam2/branches/meme/debian/compat (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/compat 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1 @@
+9
Added: trunk/packages/glam2/branches/meme/debian/control
===================================================================
--- trunk/packages/glam2/branches/meme/debian/control (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/control 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,33 @@
+Source: glam2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libfftw3-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/glam2/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/glam2/trunk/
+Homepage: http://bioinformatics.org.au/glam2/
+
+Package: glam2
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ python
+Description: gapped protein motifs from unaligned sequences
+ GLAM2 is a software package for finding motifs in sequences, typically
+ amino-acid or nucleotide sequences. A motif is a re-occurring sequence
+ pattern: typical examples are the TATA box and the CAAX prenylation motif. The
+ main innovation of GLAM2 is that it allows insertions and deletions in motifs.
+ .
+ This package includes programs for discovering motifs shared by a set of
+ sequences and finding matches to these motifs in a sequence database, as well
+ as utilities for converting glam2 motifs to standard alignment formats,
+ masking glam2 motifs out of sequences so that weaker motifs can be found, and
+ removing highly similar members of a set of sequences.
+ .
+ In this binary package, the fast Fourier algorithm (FFT) was enabled for the
+ glam2 program.
Added: trunk/packages/glam2/branches/meme/debian/copyright
===================================================================
--- trunk/packages/glam2/branches/meme/debian/copyright (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/copyright 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,124 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: glam2
+Upstream-Contact: Martin Frith <martin at cbrc.jp>,
+ Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Source: ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/
+Comment: Glam2 is maintained upstream now as part of the MEME software
+ package. While MEME is non-free upstream has agreed in the mailing
+ list thread starting here
+ http://lists.alioth.debian.org/pipermail/debian-med-packaging/2013-January/018334.html
+ to keep the old license that was used by the separate glam distribution.
+ To accomplish this the full MEME source is downloaded here but stripped
+ from all non-free parts.
+Files-Excluded:
+ config/
+ doc/examples/compute_prior_dist_example_output_files
+ doc/examples/sample_opal_scripts
+ doc/examples/[A-Zc-fh-rz-z]*
+ doc/examples/sample-[a-fh-z]*
+ doc/examples/s[b-z]*
+ doc/[A-FH-Za-fh-z]*
+ doc/g[a-km-z]*
+ etc/[A-FH-Za-fh-z]*
+ etc/g[a-km-z]*
+ scripts/[A-FH-Za-fh-z]*
+ scripts/g[a-km-z]*
+ src/[A-FH-Zdfjklnopqtv-z]*
+ src/a[a-km-qs-z]*
+ src/al[a-oq-z]*
+ src/alph[b-z]*
+ src/b[a-hj-z]*
+ src/bin[b-z]*
+ src/c[a-df-z]*
+ src/ce[a-pr-z]*
+ src/e[a-oq-z]*
+ src/g[a-km-z]*
+ src/h[b-z]*
+ src/hash[^_]*
+ src/hash_[b-z]*
+ src/hash_*.c
+ src/i[a-np-z]*
+ src/m[b-np-z]*
+ src/ma[abd-su-z]*
+ src/mat[a-qs-z]*
+ src/moti[a-eg-z]*
+ src/motif-in-[a-eg-z]*
+ src/motif-in-s[a-oq-z]*
+ src/motif-in.c
+ src/motif[_a-z]*
+ src/r[a-df-z]*
+ src/re[a-cefh-z]*
+ src/red[a-z]*
+ src/reg[a-df-z]*
+ src/s[a-su-z]*
+ src/st[a-qs-z]*
+ src/str[a-hj-z]*
+ src/string-[ac-km-z]*
+ src/string-list.c
+ src/u[a-ru-z]*
+ src/ut[a-hj-z]*
+ tests/
+ website/
+ [A-Za-c]*
+
+Files: *
+Copyright: 2007 Martin C Frith <martin at cbrc.jp>
+ 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
+License: PD
+ GLAM2 was developed by Martin C Frith, working at the Computational Biology
+ Research Center in Tokyo, and Timothy L Bailey, working at the Institute for
+ Molecular Bioscience in Brisbane. The source code and documentation are hereby
+ released into the public domain. If you use GLAM2, please cite: MC Frith, NFW
+ Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary
+ insertions and deletions, PLoS Computational Biology (PLoS Comput Biol. 2008
+ Apr 25;4(4):e1000071.).
+
+Files: purge/*
+Copyright: 2005 Andrew Neuwald
+License: PD_purge
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software is freely available to the
+ public for use. The National Library of Medicine and the U.S. Government
+ have not placed any restriction on its use or reproduction.
+ .
+ Although reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite
+ .
+ Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling:
+ detection of bacterial outer membrane protein repeats"
+ Protein Science 4, 1618-1632. (for Gibbs site sampling,
+ Gibbs motif sampling, purge, and scan programs)
+ .
+ and
+ .
+ Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993)
+ "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy
+ for Multiple Alignment", Science 262:208-214. (for Gibbs
+ site sampling program)
+ .
+ in any work or product based on this material.
+ .
+ The data structures used in this program are part of a package
+ of C code for molecular biological applications being developed
+ by A. F. Neuwald.
+
+Files: debian/*
+Copyright: 2007 Steffen Möller <moeller at debian.org>
+ 2007-2009 Charles Plessy <plessy at debian.org>
+ 2011-2013 Andreas Tille <tille at debian.org>
+License: PD_as_well
+ The package is in the public domain and so shall then be
+ the packaging for Debian of Steffen Moeller <moeller at debian.org>
+ and Charles Plessy <plessy at debian.org>.
Added: trunk/packages/glam2/branches/meme/debian/debian-compile/Makefile
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-compile/Makefile (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-compile/Makefile 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,105 @@
+# This file holds commands for compiling programs in the GLAM2 package
+
+# These commands are customized for the gcc compiler, and may need to
+# be modified for other compilers
+
+# -Wall means turn on compiler warnings (optional)
+# -O3 means optimization level 3 (the maximum for gcc)
+# -lm means include the math library
+
+# Source files for glam2:
+GSRC = glam2_alphabet.c \
+ glam2_args.c \
+ glam2_column_sample.c \
+ glam2_dirichlet.c \
+ glam2_dna_prior.c \
+ glam2_fasta.c \
+ glam2_glam2.c \
+ glam2_glam2_aln.c \
+ glam2_init.c \
+ glam2_output.c \
+ glam2_recode3_20comp.c \
+ glam2_site_sample.c \
+ glam2_util.c \
+ alphabet.c \
+ array.c \
+ array-list.c \
+ binary-search.c \
+ ceqlogo.c \
+ eps2png.c \
+ io.c \
+ matrix.c \
+ motif.c \
+ red-black-tree.c \
+ regex-utils.c \
+ string-builder.c \
+ utils.c
+
+# Source files for glam2scan:
+SSRC = glam2_alphabet.c \
+ glam2_scan_args.c \
+ glam2_dirichlet.c \
+ glam2_dna_prior.c \
+ glam2_fasta.c \
+ glam2_scan.c \
+ glam2_scan_init.c \
+ glam2_scan_output.c \
+ glam2_recode3_20comp.c \
+ glam2_util.c \
+ glam2_heap.c \
+ glam2_motif.c \
+ glam2_alignment.c \
+ utils.c
+
+# Source files for glam2format:
+FSRC = glam2_glam2format.c \
+ glam2_alignment.c \
+ glam2_fasta.c \
+ glam2_util.c \
+ utils.c
+
+# Source files for glam2mask:
+MSRC = glam2_glam2mask.c \
+ glam2_alignment.c \
+ glam2_fasta.c \
+ glam2_util.c \
+ utils.c
+
+# Compiler options:
+CFLAGS += -Wall -O3
+
+BINS = glam2 \
+ glam2scan \
+ glam2format \
+ glam2mask \
+ glam2fft
+
+all: $(BINS)
+
+# Command for compiling glam2:
+glam2: $(GSRC) *.h Makefile
+ cc $(CFLAGS) -o glam2 $(GSRC) -lm $(LDFLAGS)
+
+# Command for compiling glam2scan:
+glam2scan: $(SSRC) *.h Makefile
+ cc $(CFLAGS) -o glam2scan $(SSRC) -lm $(LDFLAGS)
+
+# Command for compiling glam2format:
+glam2format: $(FSRC) *.h Makefile
+ cc $(CFLAGS) -o glam2format $(FSRC) -lm $(LDFLAGS)
+
+# Command for compiling glam2mask:
+glam2mask: $(MSRC) *.h Makefile
+ cc $(CFLAGS) -o glam2mask $(MSRC) -lm $(LDFLAGS)
+
+# Here follow commands for compiling special versions of the programs
+
+# Compile glam2 including FFT algorithm (requires FFTW to be installed):
+glam2fft: $(GSRC) glam2_convolve.c *.h Makefile
+ cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) glam2_convolve.c -lm -lfftw3 $(LDFLAGS)
+
+clean:
+ rm -f *.o
+
+distclean:
+ rm -f $(BINS)
Added: trunk/packages/glam2/branches/meme/debian/debian-compile/config.h
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-compile/config.h (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-compile/config.h 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,6 @@
+/* Version number of package */
+#define VERSION "4.9.1"
+
+#define CONVERT_PATH "/usr/bin/convert"
+
+#define GHOSTSCRIPT_PATH "/usr/bin/gs"
Added: trunk/packages/glam2/branches/meme/debian/debian-compile/dir.h
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-compile/dir.h (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-compile/dir.h 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,4 @@
+/* #define MEME_DIR "/usr/bin" */
+#define ETC_DIR "/etc/meme"
+#define BIN_DIR "/usr/bin"
+
Added: trunk/packages/glam2/branches/meme/debian/debian-compile/glam2_convolve.c
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-compile/glam2_convolve.c (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-compile/glam2_convolve.c 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,89 @@
+/**************************************************************
+ * Taken over from old glam2 source but does not help since *
+ * glam2_convolve.h tries to include glam2_fftw3.h which is *
+ * missing and was not part of the old glam2 distribution. *
+ * Andreas Tille <tille at debian.org> *
+ **************************************************************/
+#include <assert.h>
+#include <errno.h>
+#include "glam2_util.h"
+#include "glam2_convolve.h"
+
+/* Return the lowest power of 2 that is >= x (and >= 1) */
+static int next_pow2(const int x) {
+ int y = 1;
+ while (y < x) {
+ assert(can_mul_int(y, 2));
+ y *= 2;
+ }
+ return y;
+}
+
+/* Multiplication of complex numbers */
+/* Allows output to overwrite input */
+static void multiply_complex(fftw_complex z, const fftw_complex x, const fftw_complex y) {
+ const double a = x[0] * y[0] - x[1] * y[1];
+ const double b = x[0] * y[1] + x[1] * y[0];
+ z[0] = a;
+ z[1] = b;
+}
+
+/* Dot product of complex vectors */
+/* Can't use const for pointer-to-pointer */
+static void dot_complex(fftw_complex *z, fftw_complex *x, fftw_complex *y, int size) {
+ int i;
+ for (i = 0; i < size; ++i)
+ multiply_complex(z[i], x[i], y[i]);
+}
+
+/* malloc or die */
+static void *fftw_xmalloc(size_t size) {
+ void *p = fftw_malloc(size);
+ if (p == NULL)
+ die("%s: error allocating %lu bytes: %s\n",
+ prog_name, (unsigned long)size, strerror(errno));
+ return p;
+}
+
+void fft_init(fft_convolver *f, const int max_size) {
+ int zero_pad, size, mem;
+ assert(max_size > 0);
+ zero_pad = max_size - 1; /* padding to avoid wraparound convolution */
+ assert(can_add_int(max_size, zero_pad));
+ size = next_pow2(max_size + zero_pad); /* power-of-2 size is faster??? */
+ assert(can_mul_int(2, size / 2 + 1));
+ mem = 2 * (size / 2 + 1); /* padding for in-place transforms */
+
+ f->size = size;
+
+ f->x = fftw_xmalloc(mem * sizeof(double));
+ f->y = fftw_xmalloc(mem * sizeof(double));
+ f->z = fftw_xmalloc(mem * sizeof(double));
+
+ f->x_plan = fftw_plan_dft_r2c_1d(size, f->x, (fftw_complex *)f->x,
+ FFTW_MEASURE);
+ f->y_plan = fftw_plan_dft_r2c_1d(size, f->y, (fftw_complex *)f->y,
+ FFTW_MEASURE);
+ f->z_plan = fftw_plan_dft_c2r_1d(size, (fftw_complex *)f->z, f->z,
+ FFTW_MEASURE);
+}
+
+void fft_convolve(double *z, const double *x, const double *y, const int size, fft_convolver *f) {
+ const int half_size = f->size / 2 + 1;
+ const int pad_size = f->size - size;
+ assert(size <= f->size / 2);
+
+ COPY(f->x, x, size);
+ COPY(f->y, y, size);
+ set_dbl(f->x + size, pad_size, 0); /* pad with zeros */
+ set_dbl(f->y + size, pad_size, 0); /* pad with zeros */
+
+ fftw_execute(f->x_plan);
+ fftw_execute(f->y_plan);
+ dot_complex((fftw_complex *)f->z, (fftw_complex *)f->x, (fftw_complex *)f->y,
+ half_size);
+ fftw_execute(f->z_plan);
+ mul_dbl(f->z, f->size, 1.0 / f->size);
+
+ COPY(z, f->z, size);
+}
Added: trunk/packages/glam2/branches/meme/debian/debian-docs/index.html
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-docs/index.html (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-docs/index.html 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,106 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+ "http://www.w3.org/TR/html4/strict.dtd">
+<html lang=en>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<title>GLAM2 Manual</title>
+<link type="text/css" rel="stylesheet" href="glam2.css">
+</head>
+<body>
+
+<h1>GLAM2 Manual</h1>
+
+<p><strong>Summary:</strong> GLAM2 is a software package for finding
+<em>motifs</em> in sequences, typically amino-acid or nucleotide
+sequences. A motif is a re-occurring sequence pattern: typical
+examples are the TATA box and the CAAX prenylation motif. The main
+innovation of GLAM2 is that it allows insertions and deletions in
+motifs.</p>
+
+<p><strong>Family:</strong> GLAM2 is a child of <a
+href="http://zlab.bu.edu/glam/">GLAM</a> and a sibling of <a
+href="ftp://ftp.ncbi.nih.gov/pub/spouge/papers/archive/AGLAM/">A-GLAM</a>.
+If you are looking for nucleotide motifs without insertions or
+deletions, A-GLAM is probably better. 'GLAM' used to stand for
+Gapless Local Alignment of Multiple sequences, but it now stands for
+Gapped Local Alignment of Motifs.</p>
+
+<p<strong>Inventory:</strong> The package includes these programs:</p>
+
+<ul>
+
+<li><strong>glam2</strong> - for discovering motifs shared by a set of
+sequences.</li>
+
+<li><strong>glam2scan</strong> - for finding matches, in a sequence
+database, to a motif discovered by glam2.</li>
+
+<li><strong>glam2format</strong> - for converting glam2 motifs to
+standard alignment formats.</li>
+
+<li><strong>glam2mask</strong> - for masking glam2 motifs out of
+sequences, so that weaker motifs can be found.</li>
+
+<!--
+<li><strong>purge</strong> - for removing highly similar members of a
+set of sequences.</li>
+-->
+</ul>
+
+<p>These are <em>command line</em> programs, so you need a basic
+familiarity with running things from your computer's command line in
+order to use them. (In Mac OS X, you want Applications -> Utilities ->
+Terminal.)</p>
+
+<p><strong>About:</strong> GLAM2 was developed by <a
+href="http://www.cbrc.jp/~martin/">Martin C Frith</a>, working at the
+<a href="http://www.cbrc.jp/index.eng.html">Computational Biology
+Research Center</a> in Tokyo, and <a
+href="http://research.imb.uq.edu.au/~tbailey/">Timothy L Bailey</a>,
+working at the <a href="http://www.imb.uq.edu.au/">Institute for
+Molecular Bioscience</a> in Brisbane. The source code and
+documentation are hereby released into the public domain. If you use
+GLAM2, please cite:
+<cite>MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering
+sequence motifs with arbitrary insertions and deletions, PLoS
+Computational Biology (in press)</cite>.</p>
+
+<p><strong>Contact:</strong> Questions and comments are welcome.
+Email: glam2(at-mark)imb.uq.edu.au. We would especially like to hear
+about any errors when installing or running the software
+(e.g. segmentation faults, assertion failures) so that we can fix
+them. Please send the exact text of the error message, and the exact
+inputs that produce the error.</p>
+
+<h2>Contents</h2>
+
+<ul>
+
+<li><a href="install.html">Installation</a> - how to install GLAM2 on
+your computer.</li>
+
+<li><a href="glam2_tut.html">glam2 tutorial</a> - all you need to know
+for typical usage of glam2.</li>
+
+<li><a href="glam2_ref.html">glam2 reference</a> - all of glam2's
+options.</li>
+
+<li><a href="glam2scan.html">glam2scan manual</a></li>
+
+<li><a href="glam2format.html">glam2format manual</a></li>
+
+<li><a href="glam2mask.html">glam2mask manual</a></li>
+
+<li><a href="purge.html">purge manual</a></li>
+
+<li><a href="alphabet.html">Alphabets</a></li>
+
+<li><a href="dirichlet.html">Dirichlet mixtures</a></li>
+
+<li><a href="GLAM2_method.pdf">GLAM2 methods (PDF)</a> - mathematical
+description of how GLAM2 works.</li>
+
+</ul>
+
+</body>
+</html>
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/crp0.s
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/crp0.s (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/crp0.s 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,54 @@
+>ce1cg 17 61
+TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTTCACAA
+AAATGGAAGTCCACAGTCTTGACAG
+>ara 17 55
+GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCT
+ATGCCATAGCATTTTTATCCATAAG
+>bglr1 76
+ACAAATCCCAATAACTTAATTATTGGGATTTGTTATATATAACTTTATAAATTCCTAAAATTACACAAAGTTAATAACTG
+TGAGCATGGTCATATTTTTATCAAT
+>crp 63
+CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGACGTCAC
+ATTACCGTGCAGTACAGTTGATAGC
+>cya 50
+ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACCATT
+TTTTCGTCGTGAAACTAAAAAAACC
+>deop2 7 60
+AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATCGAAGT
+GTGTTGCGGAGTAGATGTTAGAATA
+>gale 42
+GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATG
+CTATGGTTATTTCATACCATAAGCC
+>ilv 39
+GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAAAATTT
+TCCATTGTCTCCCCTGTAAAGCTGT
+>lac 9 80
+AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGG
+AATTGTGAGCGGATAACAATTTCAC
+>male 14
+ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGGTTGCC
+GTATAAAGAAACTAGAGTCCGTTTA
+>malk 29 61
+GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCTTGCAA
+AAATCGTGGCGATTTTATGTGCGCA
+>malt 41
+GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAAAACGT
+CATCGCTTGCATTAGAAAGGTTTCT
+>ompa 48
+GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGTTTTCA
+ACTACGTTGTAGACTTTACATCGCC
+>tnaa 71
+TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTGTGATT
+CGATTCACATTTAAACAATTTCAGA
+>uxu1 17
+CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAGAACTT
+ATACGCCATCTCATCCGATGCAAGC
+>pbr322 53
+CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAA
+GGAGAAAATACCGCATCAGGCGCTC
+>trn9cat 1 84
+CTGTGACGGAAGATCACTTCGCAGAATAAATAAATCCTGGTGTCCCTGTTGATACCGGGAAGCCCTGGGCCAACTTTTGG
+CGAAAATGAGACGTTGATCGGCACG
+>tdc 78
+GATTTTTATACTTTAACTTGTTGATATTTAAAGGTATTTAATTGTAATAACGATACTCTGGAAAGTATTGAAAGTTAATT
+TGTGAGTGGTCGCACATATCCTGTT
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/dna.alph
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/dna.alph (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/dna.alph 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,7 @@
+# This is the standard nucleotide alphabet.
+
+aA
+cC
+gG
+tTuU
+N
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/glam_tfbs.1comp
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/glam_tfbs.1comp (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/glam_tfbs.1comp 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,8 @@
+comment= This is a simple Dirichlet mixture with just one component, suitable
+comment= for transcription factor binding sites in DNA. It was obtained by
+comment= fitting to motifs in the TRANSFAC database, as described in: MC
+comment= Frith, U Hansen, JL Spouge, Z Weng Nucleic Acids Research 2004
+comment= 32:189-200.
+
+Mixture= 1
+Alpha= 1.6 0.4 0.4 0.4 0.4
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/lipocalin.s
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/lipocalin.s (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/lipocalin.s 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,20 @@
+>ICYA_MANSE
+GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA
+KYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVDNVLKTFSHLI
+DASKFISNDFSEAACQYSTTYSLTGPDRH
+>LACB_BOVIN
+MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENG
+ECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALP
+MHIRLSFNPTQLEEQCHI
+>BBP_PIEBR
+NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDSK
+IGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLIGSPVVDSQKL
+VYSDFSEAACKVN
+>RETB_BOVIN
+ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTDT
+EDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQKIVRQRQEELC
+LARQYRLIPHNGYCDGKSERNIL
+>MUP2_MOUSE
+MKMLLLLCLGLTLVCVHAEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGNFRLFLEQIHVLEKSLVLKFHTVRDE
+ECSELSMVADKTEKAGEYSVTYDGFNTFTIPKTDYDNFLMAHLINEKDGETFQLMGLYGREPDLSSDIKERFAKLCEEHG
+ILRENIIDLSNANRCLQARE
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/recode3.20comp
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/recode3.20comp (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/recode3.20comp 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,107 @@
+ClassName = DirichletReg
+Name = recode3.20comp
+Alphabet = ExtAA
+Order = A C D E F G H I K L M N P Q R S T V W Y
+AlphaChar= 20
+NumDistr= 20
+
+Number= 0
+Mixture= 0.176513
+Alpha= 10.1329 0.668781 0.072626 1.08101 0.930936 0.1235 0.982387 0.366701 0.0586812 0.849019 0.185073 0.0648062 0.979541 0.519704 0.555784 0.636552 1.04987 0.60931 0.129148 0.0676805 0.201772
+Comment= N , D S Q H K E G R T P >< A Y , W C F M , L V , I
+
+Number= 1
+Mixture= 0.207622
+Alpha= 11.6836 0.880009 0.197393 0.303744 0.497357 0.657492 0.391988 0.348159 0.936094 0.527206 1.42844 0.449302 0.368825 0.384576 0.439775 0.581516 0.622624 0.747064 1.08007 0.235012 0.606928
+Comment= M Y L F I W V H T Q >< R A C S K N P E , G D
+
+Number= 2
+Mixture= 0.0669246
+Alpha= 5.22319 0.153384 0.0520756 0.0073824 0.0158439 0.428964 0.025533 0.0185789 0.845361 0.0282996 2.42256 0.424296 0.0190716 0.0313429 0.0274578 0.0252186 0.028514 0.0519217 0.522946 0.0279653 0.0664755
+Comment= L , M I , F V >< C , A Y W , T H Q P , R K S N G , E , D
+
+Number= 3
+Mixture= 0.0868259
+Alpha= 9.82176 0.794007 0.0130659 0.624236 1.85769 0.0290214 0.115707 0.123504 0.22099 1.52605 0.341371 0.111114 0.308302 0.263545 0.953727 0.933444 0.554741 0.604551 0.396451 0.00823516 0.0420054
+Comment= E K Q , R T D A >< S N P V H M , L I , G , Y C F , W
+
+Number= 4
+Mixture= 0.0593123
+Alpha= 5.54386 0.740015 0.187165 0.0213261 0.0456854 0.118944 0.0633687 0.0170331 1.06684 0.0380614 0.733524 0.138456 0.0300644 0.0718692 0.0240143 0.0301022 0.0862989 0.367283 1.70735 0.0113856 0.045079
+Comment= V , I , C A L T M >< F , P S , Y G W E H , N K Q R D
+
+Number= 5
+Mixture= 0.0358616
+Alpha= 4.66847 0.15978 0.0261585 0.0505181 0.125524 0.0350331 0.102549 0.157461 0.0795041 1.26261 0.189383 0.0550608 0.171028 0.0844169 0.290476 1.44604 0.129158 0.138972 0.0851144 0.0159134 0.0637679
+Comment= R K ,, Q H >< N T M , S L A E P Y C G I V , W D F
+
+Number= 6
+Mixture= 0.03427
+Alpha= 5.9237 0.308434 0.0137217 1.69731 1.92422 0.0361113 0.162357 0.07232 0.0487895 0.236135 0.0809074 0.0286236 0.213663 0.181631 0.320245 0.104878 0.218398 0.141668 0.0747719 0.0141705 0.0453433
+Comment= E D ,, Q >< N K A P S , H T G R , M Y V W L F I C
+
+Number= 7
+Mixture= 0.0428319
+Alpha= 0.0441636 0.00260287 9.99856e-06 0.00631292 0.00445502 0.00274753 1.03886e-05 1.02839e-05 0.000913052 0.0029241 0.00353485 0.00105128 0.00338172 1.04172e-05 0.00173574 0.00459583 0.00274255 0.00247625 0.00175366 1.02411e-05 0.00288489
+Comment= D R , Y N E F K M Q T S >< L A V , I ,,,,, W C H , P , G
+
+Number= 8
+Mixture= 0.047875
+Alpha= 3.87573 1.61043 0.15522 0.0378292 0.0498243 0.0406484 0.529136 0.0217524 0.040597 0.0413396 0.100193 0.0509779 0.0357917 0.0931204 0.0367156 0.0330646 0.529587 0.196607 0.230878 0.00909518 0.0329275
+Comment= A , S C , G >< T V M P , L Q F , Y H N E K I R D W
+
+Number= 9
+Mixture= 0.0466614
+Alpha= 4.02936 0.15525 0.0136827 0.0857138 0.0508316 0.0151451 3.10555 0.027169 0.0140491 0.0654038 0.0257501 0.00901049 0.127437 0.0423873 0.0345064 0.0477247 0.12452 0.0341196 0.0230637 0.00930115 0.0187464
+Comment= G ,,,>< N S A , D K H , R Q P E C T W Y , M F V L , I
+
+Number= 10
+Mixture= 0.0283695
+Alpha= 4.37516 0.225739 0.0684326 0.101072 0.0813791 0.0298832 0.0915218 0.0336807 0.0833114 0.0931673 0.0731542 0.0419314 0.230216 0.087446 0.0694702 0.0751969 1.13857 1.63158 0.179083 0.00912576 0.0311963
+Comment= T S ,, N >< C A V , M Q P D K R I H E G , Y L F W
+
+Number= 11
+Mixture= 0.0301127
+Alpha= 5.10487 1.3431e-06 0.0166656 0.00743068 1.34592e-06 0.169076 0.00407061 0.00714122 1.98221 0.017522 0.816669 0.114773 0.00678027 0.0106392 0.0100244 0.0158968 0.00879658 0.0399043 1.81043 0.0150671 0.0517801
+Comment= I V ,, L M >< F , Y , W C T ,, R K H Q P , N S D , G ,,,,,,,,,,, E , A
+
+Number= 12
+Mixture= 0.0233828
+Alpha= 3.08488 0.063525 0.0288391 1.09265 0.0959581 0.00965196 0.216914 0.0730986 0.0207325 0.08719 0.0315107 0.00960293 0.752755 0.059914 0.0445321 0.0312317 0.287327 0.116896 0.0249446 0.00701663 0.0305859
+Comment= D N ,, S >< H G T C , K E P Q Y A , R W M , V L I F
+
+Number= 13
+Mixture= 0.034662
+Alpha= 5.72698 0.294281 0.019271 0.12293 0.162747 0.0373667 0.145029 0.0412349 0.0815261 0.157594 0.151631 0.021412 0.0601581 3.6966 0.0809085 0.101856 0.23533 0.135424 0.140532 0.00900473 0.0321389
+Comment= P ,,,>< S A , K E T Q D R V G H L , N I C M Y F , W
+
+Number= 14
+Mixture= 0.0270202
+Alpha= 3.67648 0.0844832 0.0584945 0.0411628 0.045719 0.847822 0.0590839 0.250253 0.0675757 0.0562614 0.168617 0.0439737 0.0794234 0.028301 0.0305672 0.0598024 0.0798202 0.0585385 0.0858243 0.227395 1.30336
+Comment= Y , F W , H ,>< C M L , N S V R I A T K , Q G E D P
+
+Number= 15
+Mixture= 0.0226822
+Alpha= 3.08684 0.0634034 0.0246167 1.3443e-06 0.00389272 1.12953 0.00796028 1.35032e-06 0.233395 1.34466e-06 0.541933 0.101309 1.36412e-06 0.027467 0.00704479 0.00802297 0.0248977 0.0276933 0.185467 0.183309 0.516892
+Comment= F , Y , W , L M I >< V , C A , P T S ,, Q R G , E ,,,,,,,,,, H , N K , D
+
+Number= 16
+Mixture= 0.00898452
+Alpha= 2.51284 0.123696 0.0454619 0.0386434 0.351847 0.0560181 0.0439442 0.223229 0.01302 0.148699 0.19001 0.120964 0.098734 5.90055e-06 0.554971 0.219233 0.0453885 0.0564686 0.0614792 0.0410248 0.0800036
+Comment= Q , H E M , R W K >< C N Y L A F , T V S D , G , I ,,,,,,,,,,, P
+
+Number= 17
+Mixture= 0.00716226
+Alpha= 3.39257 0.0212037 3.18769 0.00745627 0.00382411 0.00691924 0.0126233 1.34375e-06 0.00724293 0.00522979 0.00785563 0.00489521 0.0105326 0.0136265 0.00505819 0.00677712 0.0251744 0.0235516 0.0371462 0.00187667 0.0038893
+Comment= C ,,,,,><,, V T , S P A N M , G F Q R D W I Y , K L E ,,,,,,,,,, H
+
+Number= 18
+Mixture= 0.00710292
+Alpha= 2.51689 0.0229376 0.00427768 0.00959934 0.013608 0.182277 0.0227654 0.0157344 0.0226783 0.011561 0.0803491 0.0154283 0.00899225 0.00980608 0.00600945 0.0342359 0.0216842 0.0189306 0.0223176 1.83914 0.154565
+Comment= W ,,,,, F Y ><, L M R H , I S T , V G A C E P N K D Q
+
+Number= 19
+Mixture= 0.00582299
+Alpha= 1.35874 2.16602e-06 2.16245e-06 0.0198496 2.17942e-06 0.0246741 2.47051e-06 1.02563 0.0131152 2.16539e-06 0.00637704 2.1414e-06 0.0839371 0.0168135 0.0438887 0.0252951 0.0235533 0.0130626 0.00797507 2.16433e-06 0.0545531
+Comment= H ,,,, N Y >< Q , F R S P D , T I , V , L ,,,,,,,,, W C M ,, K E G A
+EndClassName = DirichletReg
Added: trunk/packages/glam2/branches/meme/debian/debian-examples/robinson.alph
===================================================================
--- trunk/packages/glam2/branches/meme/debian/debian-examples/robinson.alph (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/debian-examples/robinson.alph 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,25 @@
+# This is the standard protein alphabet. The abundances are taken
+# from from: AB Robinson & LR Robinson Proc Natl Acad Sci 1991
+# 88:8880-4, which is cited in publications on NCBI BLAST.
+
+Aa 35155
+Cc 8669
+Dd 24161
+Ee 28354
+Ff 17367
+Gg 33229
+Hh 9906
+Ii 23161
+Kk 25872
+Ll 40625
+Mm 10101
+Nn 20212
+Pp 23435
+Qq 19208
+Rr 23105
+Ss 32070
+Tt 26311
+Vv 29012
+Ww 5990
+Yy 14488
+x
Added: trunk/packages/glam2/branches/meme/debian/docs
===================================================================
--- trunk/packages/glam2/branches/meme/debian/docs (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/docs 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,2 @@
+doc/*
+debian/debian-docs/*
Added: trunk/packages/glam2/branches/meme/debian/examples
===================================================================
--- trunk/packages/glam2/branches/meme/debian/examples (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/examples 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1 @@
+debian/debian-examples/*
Added: trunk/packages/glam2/branches/meme/debian/glam2.doc-base.manual
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2.doc-base.manual (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2.doc-base.manual 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,13 @@
+Document: glam2-manual
+Title: GLAM2 Manual
+Author: Martin Frith, Timothy L Bailey
+Abstract: This manal covers the installation and
+ usage of GLAM2. It provides a tutorial and a reference
+ for the `glam2' program, a manual for the `glam2scan',
+ `glam2format', `glam2mask' and `purge', as well as
+ explanations about alphabets and Dirichlet mixtures.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/glam2/index.html
+Files: /usr/share/doc/glam2/*.html
Added: trunk/packages/glam2/branches/meme/debian/glam2.doc-base.method
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2.doc-base.method (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2.doc-base.method 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,9 @@
+Document: glam2-method
+Title: GLAM2 Methods
+Author: Martin C Frith
+Section: Science/Biology
+Abstract: This manual explains in detail
+ the statistical methods used in GLAM2.
+
+Format: PDF
+Files: /usr/share/doc/glam2/GLAM2_method.pdf.gz
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2-purge.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2-purge.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2-purge.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,92 @@
+.\" Title: GLAM2-PURGE
+.\" Author: Andrew Neuwald
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2\-PURGE" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2-purge \- Removes redundant sequences from a FASTA file
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR]
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2\-purge\fR
+is a modified version of Andrew Neuwald\'s
+\fBpurge\fR
+program that removes redundant sequences from a FASTA file\&. This is recommended in order to prevent highly similar sequences distorting the search for motifs\&. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user\&. The output file is named <file>\&.<score>\&. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/\-1 scoring scheme for DNA\&. Purge can also be used to mask tandem repeats\&. It uses the XNU program for this purpose\&.
+.SH "OPTIONS"
+.PP
+\fB\-n\fR
+.RS 4
+Sequences are DNA (default: protein)\&.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Use blast heuristic method (default for protein)\&.
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+Use an exhaustive method (default for DNA)\&.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Keep first sequence in the set\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Use xnu to mask protein tandem repeats\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2\fR(1),
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2scan\fR(1),
+\fBxnu\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCES"
+.PP
+Purge was written by Andy Neuwald and is described in more detail in Neuwald et al\&., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618\(en1632, 1995\&. Please cite it if you use Purge\&.
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBAndrew Neuwald\fR
+.sp -1n
+.IP "" 4
+Author of purge, renamed glam2\-purge in Debian\&.
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of Purge and GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,174 @@
+.\" Title: GLAM2
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2 \- Gapped Local Alignment of Motifs
+.SH "SYNOPSIS"
+.HP 6
+\fBglam2\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\&.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\&.
+.SH "DESCRIPTION"
+.PP
+GLAM2 is a software package for finding motifs in sequences, typically amino\-acid or nucleotide sequences\&. A motif is a re\-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif\&. The main innovation of GLAM2 is that it allows insertions and deletions in motifs\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Number of alignment runs (\fI10\fR)\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+End each run after this many iterations without improvement (\fI10000\fR)\&.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\&.
+.RE
+.PP
+\fB\-z\fR
+.RS 4
+Minimum number of sequences in the alignment (\fI2\fR)\&.
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Minimum number of aligned columns (\fI2\fR)\&.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Maximum number of aligned columns (\fI50\fR)\&.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Initial number of aligned columns (\fI20\fR)\&.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\&.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\&.02\fR)\&.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\&.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+Initial temperature (\fI1\&.2\fR)\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Cooling factor per n iterations (\fI1\&.44\fR)\&.
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+Temperature lower bound (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Print progress information at each iteration\&.
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Column\-sampling moves per site\-sampling move (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Site sampling algorithm:
+\fI0\fR=FAST
+\fI1\fR=SLOW
+\fI2\fR=FFT (\fI0\fR)\&.
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Seed for pseudo\-random numbers (\fI1\fR)\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2fft.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2fft.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2fft.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,176 @@
+.\" Title: GLAM2
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2fft \- Gapped Local Alignment of Motifs using fftw3 library
+.SH "SYNOPSIS"
+.HP 6
+\fBglam2fft\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\&.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\&.
+.SH "DESCRIPTION"
+.PP
+GLAM2 is a software package for finding motifs in sequences, typically amino\-acid or nucleotide sequences\&. A motif is a re\-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif\&. The main innovation of GLAM2 is that it allows insertions and deletions in motifs\&.
+.PP
+This version is using fftw3 library.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Number of alignment runs (\fI10\fR)\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+End each run after this many iterations without improvement (\fI10000\fR)\&.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\&.
+.RE
+.PP
+\fB\-z\fR
+.RS 4
+Minimum number of sequences in the alignment (\fI2\fR)\&.
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Minimum number of aligned columns (\fI2\fR)\&.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Maximum number of aligned columns (\fI50\fR)\&.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Initial number of aligned columns (\fI20\fR)\&.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\&.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\&.02\fR)\&.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\&.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+Initial temperature (\fI1\&.2\fR)\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Cooling factor per n iterations (\fI1\&.44\fR)\&.
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+Temperature lower bound (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Print progress information at each iteration\&.
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Column\-sampling moves per site\-sampling move (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Site sampling algorithm:
+\fI0\fR=FAST
+\fI1\fR=SLOW
+\fI2\fR=FFT (\fI0\fR)\&.
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Seed for pseudo\-random numbers (\fI1\fR)\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2format.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2format.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2format.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,86 @@
+.\" Title: GLAM2FORMAT
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2FORMAT" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2format \- converts GLAM2 motifs to FASTA or MSF format
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\&.glam2\fR
+.PP
+Formats: fasta, msf\&.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2format\fR
+reads in a motif found by
+\fBglam2\fR, and writes it in a standard alignment format (FASTA\-with\-gaps or MSF)\&. This enables the alignment to be passed to third\-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo\&. On the other hand, not all the motif information is preserved: in particular, the key positions are lost\&. Only the top motif in
+\fBglam2\fR
+output is converted\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Make a compact alignment\&. By default, residues that are inserted between key positions are written as unaligned with each other\&. This best reflects
+\fBglam2\fR\'s intention, but it can make the alignment large and full of gaps\&. With
+\fI\-c\fR, inserted residues are written as arbitrarily aligned with each other, just as they appear in the
+\fBglam2\fR
+output\&.
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Sequence file to make a
+\(lqglobal\(rq
+alignment by adding flanking sequences from the original FASTA\-format sequence file\&. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the
+\fI\-c\fR
+option\&. The sequences should have unique names and their order should be unchanged\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBboxshade\fR(1),
+\fBglam2\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2html.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2html.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2html.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,33 @@
+.TH "GLAM2HTML" "1" "06/20/2012" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2html \- convert GLAM2 output to html
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2html\fR
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2html\fR
+reads GLAM2 output from STDIN and writes HTML output to STDOUT.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2mask.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2mask.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2mask.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,73 @@
+.\" Title: GLAM2MASK
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2MASK" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2mask \- masks a GLAM2 motif in sequences
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2mask\fR [\fBoptions\fR] \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2mask\fR
+masks a
+\fBglam2\fR
+motif out of sequences, so that weaker motifs can be found\&. Masking replaces residues aligned to key positions with the symbol \'x\'\&. By alternately applying
+\fBglam2\fR
+and
+\fBglam2mask\fR
+several times, it is possible to find the strongest, second\-strongest, third\-strongest, etc\&. motifs in a set of sequences\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Mask character (\fIx\fR)\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2psfm.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2psfm.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2psfm.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,34 @@
+.TH "GLAM2PSFM" "1" "06/20/2012" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2psfm \- convert GLAM2 output to html
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2psfm\fR <filename>
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2psfm\fR
+reads glam2 output from <filename> and writes it in MEME's PSFM format.
+This can be used as input to TOMTOM.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,109 @@
+.\" Title: GLAM2SCAN
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2SCAN" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2scan \- finds a GLAM2 motif in a database
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2scan\fR [\fBoptions\fR] \fBalphabet\fR \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\&.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2scan\fR
+finds matches, in a sequence database, to a motif discovered by
+\fBglam2\fR\&. Each match receives a score, indicating how well it fits the motif\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+Number of alignments to report (\fI25\fR)\&.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\&.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\&.02\fR)\&.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan2html.1
===================================================================
--- trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan2html.1 (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/glam2_manpages/glam2scan2html.1 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,33 @@
+.TH "GLAM2SCAN2HTML" "1" "06/20/2012" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2scan2html \- convert GLAM2SCAN output to html
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2scan2html\fR
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2scan2html\fR
+reads GLAM2SCAN output from STDIN and writes an HTML output to STDOUT.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
Added: trunk/packages/glam2/branches/meme/debian/install
===================================================================
--- trunk/packages/glam2/branches/meme/debian/install (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/install 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,7 @@
+src/glam2 usr/bin
+src/glam2format usr/bin
+src/glam2mask usr/bin
+src/glam2scan usr/bin
+src/glam2fft usr/bin
+debian/tmp_py/* usr/bin
+# purge/purge /usr/bin
Added: trunk/packages/glam2/branches/meme/debian/manpages
===================================================================
--- trunk/packages/glam2/branches/meme/debian/manpages (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/manpages 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1 @@
+debian/glam2_manpages/*.1
Added: trunk/packages/glam2/branches/meme/debian/patches/fix_fftw3_build.patch
===================================================================
--- trunk/packages/glam2/branches/meme/debian/patches/fix_fftw3_build.patch (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/patches/fix_fftw3_build.patch 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Tue, 12 Nov 2013 15:17:01 +0100
+Description: fftw2 is no glam2 header file
+
+--- a/src/glam2_convolve.h
++++ b/src/glam2_convolve.h
+@@ -3,7 +3,7 @@
+ #ifndef GLAM2_CONVOLVE_H
+ #define GLAM2_CONVOLVE_H
+
+-#include "glam2_fftw3.h"
++#include "fftw3.h"
+
+ typedef struct {
+ int size;
Added: trunk/packages/glam2/branches/meme/debian/patches/series
===================================================================
--- trunk/packages/glam2/branches/meme/debian/patches/series (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/patches/series 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1 @@
+fix_fftw3_build.patch
Added: trunk/packages/glam2/branches/meme/debian/rules
===================================================================
--- trunk/packages/glam2/branches/meme/debian/rules (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/rules 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ dh_auto_clean
+ cd src; make distclean; for ownfile in `ls ../debian/debian-compile/*` ; do rm -f `basename $${ownfile}` ; done
+ rm -rf debian/tmp_py
+
+override_dh_auto_build:
+ cp -a debian/debian-compile/* src
+ cd src; make CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mkdir debian/tmp_py
+ for script in `ls scripts/*.py.in` ; do \
+ sed 's#@WHICHPYTHON@#/usr/bin/python#' $${script} >> debian/tmp_py/`basename $${script} .py.in` ; \
+ done
+
+# Remark: The following uscan command requires devscripts > 2.12.4 which is not
+# yet released at the time of this package release. The code can be obtained
+# via
+# git clone git://tille@git.debian.org/git/users/tille/devscripts.git
+# and then use scripts/uscan.pl
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs --repack-compression xz
Property changes on: trunk/packages/glam2/branches/meme/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/glam2/branches/meme/debian/source/format
===================================================================
--- trunk/packages/glam2/branches/meme/debian/source/format (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/source/format 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/glam2/branches/meme/debian/upstream
===================================================================
--- trunk/packages/glam2/branches/meme/debian/upstream (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/upstream 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,17 @@
+Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Homepage: http://bioinformatics.org.au/glam2/
+Name: GLAM2
+Reference:
+ author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
+ journal: PLoS Computational Biology
+ publisher: Public Library of Science
+ title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions
+ year: 2008
+ month: 05
+ volume: 4
+ DOI: 10.1371/journal.pcbi.1000071
+ PMID: 18437229
+ url: http://dx.plos.org/10.1371/journal.pcbi.1000071
+ pages: e1000071
+ number: 5
+Watch: http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip
Added: trunk/packages/glam2/branches/meme/debian/watch
===================================================================
--- trunk/packages/glam2/branches/meme/debian/watch (rev 0)
+++ trunk/packages/glam2/branches/meme/debian/watch 2013-11-20 21:53:31 UTC (rev 15193)
@@ -0,0 +1,3 @@
+version=3
+opts="uversionmangle=s/_/./,dversionmangle=s/\+dfsg//g" \
+ http://ebi.edu.au/ftp/software/MEME/index.html .*/meme[_\-](\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
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