[med-svn] r5729 - in trunk/packages/meme/trunk/debian: . glam2_manpages patches source
Andreas Tille
tille at alioth.debian.org
Fri Jan 28 17:42:49 UTC 2011
Author: tille
Date: 2011-01-28 17:42:48 +0000 (Fri, 28 Jan 2011)
New Revision: 5729
Added:
trunk/packages/meme/trunk/debian/glam2.install
trunk/packages/meme/trunk/debian/glam2.manpages
trunk/packages/meme/trunk/debian/glam2.upstream-metadata.yaml
trunk/packages/meme/trunk/debian/glam2_manpages/
trunk/packages/meme/trunk/debian/glam2_manpages/glam2-purge.1
trunk/packages/meme/trunk/debian/glam2_manpages/glam2.1
trunk/packages/meme/trunk/debian/glam2_manpages/glam2format.1
trunk/packages/meme/trunk/debian/glam2_manpages/glam2mask.1
trunk/packages/meme/trunk/debian/glam2_manpages/glam2scan.1
trunk/packages/meme/trunk/debian/source/
trunk/packages/meme/trunk/debian/source/format
Removed:
trunk/packages/meme/trunk/debian/README.Debian
trunk/packages/meme/trunk/debian/dirs
trunk/packages/meme/trunk/debian/docs
trunk/packages/meme/trunk/debian/patches/xyz.diff
Modified:
trunk/packages/meme/trunk/debian/changelog
trunk/packages/meme/trunk/debian/compat
trunk/packages/meme/trunk/debian/control
trunk/packages/meme/trunk/debian/rules
trunk/packages/meme/trunk/debian/watch
Log:
Adapted the (orphaned) packaging stuff to latest meme version, I started from the fact that glam2 is outdated but now included into meme source. To update glam2 we should probably package meme. The work is very far from beeing ready - but just a step in this direction
Deleted: trunk/packages/meme/trunk/debian/README.Debian
===================================================================
--- trunk/packages/meme/trunk/debian/README.Debian 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/README.Debian 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,8 +0,0 @@
-meme for Debian
----------------
-
-This package lacks man pages.
-
-In its current version only the binaries of meme and mast are created. The offered parallelism is not utilised and the Makefile was crippled to facilitate the packaging of this software. To improve on all these issues (and others I am likely to have neglected) I'd appreciate help for.
-
- -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 20 Jan 2005 02:36:49 +0100
Modified: trunk/packages/meme/trunk/debian/changelog
===================================================================
--- trunk/packages/meme/trunk/debian/changelog 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/changelog 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,6 +1,6 @@
-meme (3.0.13-1) unstable; urgency=low
+meme (4.5.0-1) unstable; urgency=low
* Initial Release.
- -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 20 Jan 2005 02:36:49 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 27 Jan 2011 17:42:05 +0100
Modified: trunk/packages/meme/trunk/debian/compat
===================================================================
--- trunk/packages/meme/trunk/debian/compat 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/compat 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1 +1 @@
-4
+7
Modified: trunk/packages/meme/trunk/debian/control
===================================================================
--- trunk/packages/meme/trunk/debian/control 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/control 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,24 +1,48 @@
Source: meme
Section: non-free/science
Priority: optional
-Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
-Build-Depends: debhelper (>= 4.0.0)
-Standards-Version: 3.6.1.1
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.1), quilt (>=0.47), libxslt1-dev
+Standards-Version: 3.9.1
+Homepage: http://meme.nbcr.net/meme/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/meme/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/meme/agdbnet/trunk/?rev=0&sc=0
Package: meme
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, csh
-Description: [Biology] search for common motifs in DNA or protein sequences
- MEME (Multiple EM for Motif Elicitation) discovers motifs in sequences.
+Description: search for common motifs in DNA or protein sequences
+ MEME (Multiple EM for Motif Elicitation) is a tool for discovering
+ motifs in a group of related DNA or protein sequences. A motif is a
+ sequence pattern that occurs repeatedly in a group of related protein or
+ DNA sequences. MEME represents motifs as position-dependent
+ letter-probability matrices which describe the probability of each
+ possible letter at each position in the pattern. Individual MEME motifs
+ do not contain gaps. Patterns with variable-length gaps are split by
+ MEME into two or more separate motifs.
.
- A motif is a sequence pattern that occurs repeatedly in a group
- of related protein or DNA sequences. Motifs are represented as
- position-dependent scoring matrices that describe the score of each
- possible letter at each position in the pattern. Individual motifs may
- not contain gaps but combinations of patterns may be elucidated.
+ MEME takes as input a group of DNA or protein sequences (the training set)
+ and outputs as many motifs as requested. MEME uses statistical modeling
+ techniques to automatically choose the best width, number of occurrences,
+ and description for each motif.
+
+Package: glam2
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+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.
.
- The output of MEME may be forwarded to the program MAST of this package
- for the search in sequence databases.
+ 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.
.
- Homepage: http://meme.sdsc.edu
+ In this binary package, the fast Fourier algorithm (FFT) was enabled for the
+ glam2 program.
Deleted: trunk/packages/meme/trunk/debian/dirs
===================================================================
--- trunk/packages/meme/trunk/debian/dirs 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/dirs 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,2 +0,0 @@
-usr/bin
-usr/share/meme/bin
Deleted: trunk/packages/meme/trunk/debian/docs
===================================================================
--- trunk/packages/meme/trunk/debian/docs 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/docs 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,4 +0,0 @@
-README
-WEBSITE
-debian/mast_manual.txt
-debian/meme_manual.txt
Added: trunk/packages/meme/trunk/debian/glam2.install
===================================================================
--- trunk/packages/meme/trunk/debian/glam2.install (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2.install 2011-01-28 17:42:48 UTC (rev 5729)
@@ -0,0 +1 @@
+usr/bin/glam*
Added: trunk/packages/meme/trunk/debian/glam2.manpages
===================================================================
--- trunk/packages/meme/trunk/debian/glam2.manpages (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2.manpages 2011-01-28 17:42:48 UTC (rev 5729)
@@ -0,0 +1 @@
+debian/glam2_manpages/*
Added: trunk/packages/meme/trunk/debian/glam2.upstream-metadata.yaml
===================================================================
--- trunk/packages/meme/trunk/debian/glam2.upstream-metadata.yaml (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2.upstream-metadata.yaml 2011-01-28 17:42:48 UTC (rev 5729)
@@ -0,0 +1,17 @@
+Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
+DOI: 10.1371/journal.pcbi.1000071
+Homepage: http://bioinformatics.org.au/glam2/
+Name: GLAM2
+PMID: 18437229
+Reference:
+ author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
+ journal: PLoS Comput Biol
+ publisher: Public Library of Science
+ title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions
+ year: 2008
+ month: 05
+ volume: 4
+ 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/meme/trunk/debian/glam2_manpages/glam2-purge.1
===================================================================
--- trunk/packages/meme/trunk/debian/glam2_manpages/glam2-purge.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2_manpages/glam2-purge.1 2011-01-28 17:42:48 UTC (rev 5729)
@@ -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/meme/trunk/debian/glam2_manpages/glam2.1
===================================================================
--- trunk/packages/meme/trunk/debian/glam2_manpages/glam2.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2_manpages/glam2.1 2011-01-28 17:42:48 UTC (rev 5729)
@@ -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/meme/trunk/debian/glam2_manpages/glam2format.1
===================================================================
--- trunk/packages/meme/trunk/debian/glam2_manpages/glam2format.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2_manpages/glam2format.1 2011-01-28 17:42:48 UTC (rev 5729)
@@ -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/meme/trunk/debian/glam2_manpages/glam2mask.1
===================================================================
--- trunk/packages/meme/trunk/debian/glam2_manpages/glam2mask.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2_manpages/glam2mask.1 2011-01-28 17:42:48 UTC (rev 5729)
@@ -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/meme/trunk/debian/glam2_manpages/glam2scan.1
===================================================================
--- trunk/packages/meme/trunk/debian/glam2_manpages/glam2scan.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/glam2_manpages/glam2scan.1 2011-01-28 17:42:48 UTC (rev 5729)
@@ -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
Deleted: trunk/packages/meme/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/meme/trunk/debian/patches/xyz.diff 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/patches/xyz.diff 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,239 +0,0 @@
---- meme-3.0.13.orig/src/makefile
-+++ meme-3.0.13/src/makefile
-@@ -23,94 +23,25 @@
- #
- # Compiler and linker flags.
- #
--CC = cc -O
--GCC = gcc -Wall -O3 #-g #-DEXP -pg -m64
--SUN_CC = cc -O -Xa
-+CC = gcc
-+CFLAGS = -O3
- MPICC = mpicc -DPARALLEL -O
- T3E_MPICC = cc -DPARALLEL -O3 -h msglevel_3
- RS6000_MPICC = mpcc -DPARALLEL -O3 -qstrict -qarch=pwr3 -qtune=pwr3
- IRIX_MPICC = gcc -DPARALLEL -O3
--INCLUDES = -I${SRC} -I${SRC}/INCLUDE
--XTRAFLAGS = -D${M} -DUNIX -D__USE_FIXED_PROTOTYPES__ #-DEXP
--CFLAGS = ${INCLUDES} ${XTRAFLAGS}
--
--#
--# Current directory relative to bin directory.
--#
--SRC = ../../src
--
--#
--# Create symbolic links from bin directory to src directory .c files
--# if they don't already exist.
--#
--links:
-- @ if [ "${mode}" = p ] ; then p="_p"; else p=""; fi; \
-- bin=../bin/`../bin/machid`$$p; \
-- if [ ! -d $$bin ] ; then mkdir $$bin; chmod 755 $$bin; fi; \
-- for f in *.c; do \
-- if [ ! -f $$bin/$$f ] ; then ln -s ${SRC}/$$f $$bin/$$f; fi \
-- done
--
--#
--# Make the objects and executable.
--#
--objexe:
-- @ OS=`uname -s | tr -d '[:space:'] | tr -c '[:alnum:]' '_'`; \
-- machid=`../bin/machid`; \
-- plib=""; \
-- if [ "${mode}" = p ] ; then \
-- p="_p"; \
-- if [ $$OS = "crayt3e" ] ; then \
-- cc="${T3E_MPICC}"; \
-- else \
-- if [ $$OS = "AIX" ] ; then \
-- cc="${RS6000_MPICC}"; \
-- else \
-- if [ $$OS = "IRIX64" ] ; then \
-- cc="${IRIX_MPICC}"; \
-- plib="-lmpi"; \
-- else \
-- cc="${MPICC}"; \
-- fi; \
-- fi; \
-- fi; \
-- else \
-- if [ -f `which gcc` ] ; then \
-- cc="${GCC}"; \
-- else \
-- if [ $$OS = "SunOS" ] ; then \
-- cc="${SUN_CC}"; \
-- else \
-- cc="${CC}"; \
-- fi; \
-- fi; \
-- fi; \
-- cd ../bin/$$machid$$p; \
-- make -f ${SRC}/makefile exec M=$$OS CC="$$cc ${SO}" PLIB=$$plib;
--
--#
--# Make the executable.
--#
--exec: ${OBJ}
-- @ if [ ${TAR} = readseq ] || [ ${TAR} = meme-client ] || \
-- [ ${TAR} = meme-server ] || [ ${TAR} = mast-server ] || \
-- [ ${TAR} = alphtype ]; then \
-- lib=""; \
-- else \
-- lib="-lm"; \
-- fi; \
-- if [ ${M} = SunOS ] ; then \
-- lib="$$lib -lnsl -lsocket -ldl ${PLIB}"; \
-- else \
-- lib="$$lib ${PLIB}"; \
-- fi; \
-- echo ${CC} ${OBJ} -o ${TAR} $$lib; \
-- ${CC} ${OBJ} -o ${TAR} $$lib; \
-- if [ -f ${TAR} ] ; then chmod 755 ${TAR}; fi
-+INCLUDES = -I. -IINCLUDE
-+#XTRAFLAGS = -D${M} -DUNIX -D__USE_FIXED_PROTOTYPES__ #-DEXP
-+XTRAFLAGS = -DUNIX -D__USE_FIXED_PROTOTYPES__ #-DEXP
-+
-+.SUFFIXES: .c .o
-+
-+%.o: %.c
-+ $(CC) $(CFLAGS) $(INCLUDES) $(XTRAFLAGS) -c $<
-
- #
- # Lists of objects.
- #
-+#
- SEQ_OBJECTS = hash.o hash_alph.o read_seq_file.o background.o
- MOTIF_OBJECTS = logodds.o motifs.o regress.o
- MEME_OBJECTS = clock.o display.o dpalign.o em.o \
-@@ -135,35 +66,93 @@
- DPALIGN_OBJECTS = dpalign.o meme_util.o hash_alph.o display.o
-
- #
-+# Make the executable.
-+#
-+#exec: ${OBJ}
-+# @ if [ ${TAR} = readseq ] || [ ${TAR} = meme-client ] || \
-+# [ ${TAR} = meme-server ] || [ ${TAR} = mast-server ] || \
-+# [ ${TAR} = alphtype ]; then \
-+# lib=""; \
-+# else \
-+# lib="-lm"; \
-+# fi; \
-+# if [ ${M} = SunOS ] ; then \
-+# lib="$$lib -lnsl -lsocket -ldl ${PLIB}"; \
-+# else \
-+# lib="$$lib ${PLIB}"; \
-+# fi; \
-+# echo $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) ${OBJ} -o ${TAR} $$lib; \
-+# $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) ${OBJ} -o ${TAR} $$lib; \
-+# if [ -f ${TAR} ] ; then chmod 755 ${TAR}; fi
-+#
-+
-+#
- # Targets.
- #
--meme: links
-- @ make -f makefile objexe OBJ="${MEME_OBJECTS}" TAR=$@
--dpalign: links
-- @ make -f makefile objexe OBJ="${DPALIGN_OBJECTS}" TAR=$@
--llr: links
-- @ make -f makefile objexe SO="-DSO" OBJ="${LLR_OBJECTS}" TAR=$@
--star: links
-- @ make -f makefile objexe SO="-DSO" OBJ="${STAR_OBJECTS}" TAR=$@
--ic: links
-- @ make -f makefile objexe SO="-DSO" OBJ="${IC_OBJECTS}" TAR=$@
--mast: links
-- @ make -f makefile objexe OBJ="${MAST_OBJECTS}" TAR=$@
--siteroc: links
-- @ make -f makefile objexe OBJ="${SITEROC_OBJECTS}" TAR=$@
--seqroc: links
-- @ make -f makefile objexe OBJ="${SEQROC_OBJECTS}" TAR=$@
--getsize: links
-- @ make -f makefile objexe OBJ="${GETSIZE_OBJECTS}" TAR=$@
--meme-client: links
-- @ make -f makefile objexe OBJ="${MEME-CLIENT_OBJECTS}" TAR=$@
--meme-server: links
-- @ make -f makefile objexe OBJ="${MEME-SERVER_OBJECTS}" TAR=$@
--mast-server: links
-- @ make -f makefile objexe OBJ="${MAST-SERVER_OBJECTS}" TAR=$@
--readseq: links
-- @ make -f makefile objexe OBJ="${READSEQ_OBJECTS}" TAR=$@
--alphtype: links
-- @ make -f makefile objexe OBJ="${ALPHTYPE_OBJECTS}" TAR=$@
-+
-+#TARGETS=meme dpalign llr star ic mast siteroc seqroc getsize meme-client meme-server mast-server \
-+ readseq alphtype
-+TARGETS=meme mast
-+
-+all: $(TARGETS)
-+
-+meme: $(MEME_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(MEME_OBJECTS) -o $@ -lm
-+
-+mast: $(MAST_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(MAST_OBJECTS) -o $@ -lm
-+
-+dpalign: $(DPALIGN_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(DPALIGN_OBJECTS) -o $@
-+
-+llr: $(LLR_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(LLR_OBJECTS) -o $@
-+
-+star: $(STAR_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(STAR_OBJECTS) -o $@
-+
-+ic: $(IC_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(IC_OBJECTS) -o $@
-+
-+siteroc: $(SITEROC_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(SITEROC_OBJECTS) -o $@
-+
-+seqroc: $(SEQROC_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(SEQROC_OBJECTS) -o $@
-+
-+getsize: $(GETSIZE_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(GETSIZE_OBJECTS) -o $@
-+
-+meme-client: $(MEME-CLIENT_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(MEME-CLIENT_OBJECTS) -o $@ -lm
-+
-+meme-server: $(MEME-SERVER_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(MEME-SERVER_OBJECTS) -o $@ -lm
-+
-+mast-server: $(MAST-SERVER_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(MAST-SERVER_OBJECTS) -o $@ -lm
-+
-+readseq: $(READSEQ_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(READSEQ_OBJECTS) -o $@ -lm
-+
-+alphtype: $(ALPHTYPE_OBJECTS)
-+ $(CC) $(CFLAGS) $(INCLUDES) $(EXTRAFLAGS) $(ALPHATYE_OBJECTS) -o $@ -lm
-+
- test:
-- cd ..; bin/runtests
-+ (cd .. && bin/runtests)
-+
-+DESTDIR=/
-+
-+install: all
-+ cp -r ../bin/* $(DESTDIR)/usr/share/meme/bin/
-+ cp $(TARGETS) $(DESTDIR)/usr/share/meme/bin/
-+ (cd $(DESTDIR)/usr/bin/ && ln -s /usr/share/meme/bin/m{ast,eme} .)
-+
-+clean:
-+ rm -f *.o
-+
-+distclean: clean
-+ rm -f $(TARGETS)
-+
-+
-+.PHONY: clean distclean
---- meme-3.0.13.orig/website/cgi-bin/process_request.cgi
-+++ meme-3.0.13/website/cgi-bin/process_request.cgi
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- # process_request.cgi
-
- #
Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/rules 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,79 +1,22 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
+# debian/rules file for meme
+# Andreas Tille <tille at debian.org>
+# GPL
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+DBPATH=/var/lib/meme
+LOGPATH=/var/log/meme
+%:
+ dh $@ --with quilt
+override_dh_auto_configure:
+ ./configure --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --sysconfdir=/etc \
+ --with-logs=$(LOGPATH) --with-db=$(DBPATH)
+override_dh_auto_install:
+ # make MEME_DB=`pwd`/debian/meme/$(DBPATH) install
+ dh_auto_install -- MEME_DB=`pwd`/debian/meme/$(DBPATH)
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-configure:
-
-build: build-stamp
-build-stamp:
- dh_testdir
-
- $(MAKE) -C src
- #docbook-to-man debian/meme.sgml > meme.1
-
- touch build-stamp
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
-
- -$(MAKE) -C src distclean
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- # Add here commands to install the package into debian/meme.
- $(MAKE) -C src install DESTDIR=$(CURDIR)/debian/meme
- cp -r website $(CURDIR)/debian/meme/usr/share/meme/
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_installexamples
-# dh_installmenu
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_perl
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+override_dh_auto_clean:
+ dh_auto_clean
+ cd etc; rm -f fasta_db.csv fasta_db.index gomo_db.csv logo.js.xsl meme.css.xsl motif_db.csv motif_db.index tomtom_config.xml
Added: trunk/packages/meme/trunk/debian/source/format
===================================================================
--- trunk/packages/meme/trunk/debian/source/format (rev 0)
+++ trunk/packages/meme/trunk/debian/source/format 2011-01-28 17:42:48 UTC (rev 5729)
@@ -0,0 +1 @@
+3.0 (quilt)
Modified: trunk/packages/meme/trunk/debian/watch
===================================================================
--- trunk/packages/meme/trunk/debian/watch 2011-01-28 14:52:27 UTC (rev 5728)
+++ trunk/packages/meme/trunk/debian/watch 2011-01-28 17:42:48 UTC (rev 5729)
@@ -1,2 +1,2 @@
version=3
-ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/ meme_(.*)\.tar.gz
+http://meme.nbcr.net/downloads/meme_([\d\.]+)\.tar\.gz
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