[med-svn] r1887 - in trunk/packages/glam2/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun May 18 09:51:10 UTC 2008
Author: plessy
Date: 2008-05-18 09:51:09 +0000 (Sun, 18 May 2008)
New Revision: 1887
Added:
trunk/packages/glam2/trunk/debian/patches/CFLAGS-support.patch
Removed:
trunk/packages/glam2/trunk/debian/patches/Makefiles
Modified:
trunk/packages/glam2/trunk/debian/changelog
trunk/packages/glam2/trunk/debian/copyright
trunk/packages/glam2/trunk/debian/glam2-purge.1
trunk/packages/glam2/trunk/debian/glam2-purge.1.xml
trunk/packages/glam2/trunk/debian/glam2.1
trunk/packages/glam2/trunk/debian/glam2.1.xml
trunk/packages/glam2/trunk/debian/glam2format.1
trunk/packages/glam2/trunk/debian/glam2format.1.xml
trunk/packages/glam2/trunk/debian/glam2mask.1
trunk/packages/glam2/trunk/debian/glam2mask.1.xml
trunk/packages/glam2/trunk/debian/glam2scan.1
trunk/packages/glam2/trunk/debian/glam2scan.1.xml
trunk/packages/glam2/trunk/debian/install
trunk/packages/glam2/trunk/debian/patches/series
trunk/packages/glam2/trunk/debian/rules
Log:
Simplified the patch in order to submit it upstream, updated debian/copyright to the latest proposal format, and updated my address in the manpages.
Modified: trunk/packages/glam2/trunk/debian/changelog
===================================================================
--- trunk/packages/glam2/trunk/debian/changelog 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/changelog 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,12 +1,18 @@
-glam2 (1058-2) UNRELEASED; urgency=low
+glam2 (1062-1) UNRELEASED; urgency=low
- [ Andreas Tille ]
- * Better formatting of long description.
-
[ Charles Plessy ]
+ * New upstream release.
* 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:
+ - does not rename the binaries anymore (it is done in debian/rules).
+ - does not change the default optimisation level anymore.
+ - is renamed debian/patches/CFLAGS-support.patch as it is only doing this.
+ [ Andreas Tille ]
+ * Better formatting of long description.
+
-- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 16:58:37 +0900
glam2 (1058-1) unstable; urgency=low
Modified: trunk/packages/glam2/trunk/debian/copyright
===================================================================
--- trunk/packages/glam2/trunk/debian/copyright 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/copyright 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,17 +1,23 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Steffen Moeller <moeller at debian.org>
-X-Debianized-Date: Tue, 13 Nov 2007 00:35:50 +0100.
-X-Source-Downloaded-From: http://bioinformatics.org.au/glam2/archive/
-X-Upstream-Author: Martin C Frith <martin at cbrc.jp>
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Steffen Moeller <moeller at debian.org>
+Debianized-Date: Tue, 13 Nov 2007 00:35:50 +0100.
+Original-Source-Location: http://bioinformatics.org.au/glam2/archive/glam2-1062.zip
+Original-Source-Depends: unzip
+Original-Source-Command: ./debian/rules get-orig-source
+Upstream-Author: Martin C Frith <martin at cbrc.jp>
Timothy L Bailey <t.bailey at imb.uq.edu.au>
-Files: debian/*
-X-Upstream-Author: 2007 Steffen Moeller <moeller at debian.org>
- 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+Files: *
+X-Upstream-Author: 2007 Martin C Frith <martin at cbrc.jp>
+ 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
License: PD
- 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 <charles-debian-nospam at plessy.org>.
+ 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/*
X-Upstream-Author: Andrew Neuwald
@@ -54,13 +60,10 @@
of C code for molecular biological applications being developed
by A. F. Neuwald.
-Files: *
-X-Upstream-Author: 2007 Martin C Frith <martin at cbrc.jp>
- 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Files: debian/*
+Upstream-Author: 2007 Steffen Moeller <moeller at debian.org>
+ 2007-2008 Charles Plessy <plessy at debian.org>
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 (in press).
+ 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>.
Modified: trunk/packages/glam2/trunk/debian/glam2-purge.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2-purge.1 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2-purge.1 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,17 +1,17 @@
.\" Title: GLAM2-PURGE
.\" Author: Andrew Neuwald
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/26/2008
+.\" Date: 05/19/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2\-PURGE" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.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
+glam2-purge \- Removes redundant sequences from a FASTA file
.SH "SYNOPSIS"
.HP 12
\fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR]
@@ -21,32 +21,32 @@
\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\.
+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)\.
+Sequences are DNA (default: protein)\&.
.RE
.PP
\fB\-b\fR
.RS 4
-Use blast heuristic method (default for protein)\.
+Use blast heuristic method (default for protein)\&.
.RE
.PP
\fB\-e\fR
.RS 4
-Use an exhaustive method (default for DNA)\.
+Use an exhaustive method (default for DNA)\&.
.RE
.PP
\fB\-q\fR
.RS 4
-Keep first sequence in the set\.
+Keep first sequence in the set\&.
.RE
.PP
\fB\-x\fR
.RS 4
-Use xnu to mask protein tandem repeats\.
+Use xnu to mask protein tandem repeats\&.
.RE
.SH "SEE ALSO"
.PP
@@ -57,36 +57,36 @@
\fBxnu\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
-\fIhttp://bioinformatics\.org\.au/glam2/\fR
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
-\fI/usr/share/doc/glam2/\fR\.
+\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\.
+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)\.
+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\.
+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\.
+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\.
+Modified purge to be ANSI standard C and improved the user interface\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Formatted this manpage in DocBook XML for the Debian distribution\.
+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\.
+The source code and the documentation of Purge and GLAM2 are released in the public domain\&.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2-purge.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2-purge.1.xml 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2-purge.1.xml 2008-05-18 09:51:09 UTC (rev 1887)
@@ -14,7 +14,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
Modified: trunk/packages/glam2/trunk/debian/glam2.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2.1 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,129 +1,129 @@
.\" Title: GLAM2
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/26/2008
+.\" Date: 05/19/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.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
+glam2 \- Gapped Local Alignment of Motifs
.SH "SYNOPSIS"
.HP 6
-\fBglam2\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\.fa\fR
+\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\.
+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\.
+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\.
+Show all options and their default settings\&.
.RE
.PP
\fB\-o\fR
.RS 4
-Output file (\fIstdout\fR)\.
+Output file (\fIstdout\fR)\&.
.RE
.PP
\fB\-r\fR
.RS 4
-Number of alignment runs (\fI10\fR)\.
+Number of alignment runs (\fI10\fR)\&.
.RE
.PP
\fB\-n\fR
.RS 4
-End each run after this many iterations without improvement (\fI10000\fR)\.
+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\.
+Examine both strands \- forward and reverse complement\&.
.RE
.PP
\fB\-z\fR
.RS 4
-Minimum number of sequences in the alignment (\fI2\fR)\.
+Minimum number of sequences in the alignment (\fI2\fR)\&.
.RE
.PP
\fB\-a\fR
.RS 4
-Minimum number of aligned columns (\fI2\fR)\.
+Minimum number of aligned columns (\fI2\fR)\&.
.RE
.PP
\fB\-b\fR
.RS 4
-Maximum number of aligned columns (\fI50\fR)\.
+Maximum number of aligned columns (\fI50\fR)\&.
.RE
.PP
\fB\-w\fR
.RS 4
-Initial number of aligned columns (\fI20\fR)\.
+Initial number of aligned columns (\fI20\fR)\&.
.RE
.PP
\fB\-d\fR
.RS 4
-Dirichlet mixture file\.
+Dirichlet mixture file\&.
.RE
.PP
\fB\-D\fR
.RS 4
-Deletion pseudocount (\fI0\.1\fR)\.
+Deletion pseudocount (\fI0\&.1\fR)\&.
.RE
.PP
\fB\-E\fR
.RS 4
-No\-deletion pseudocount (\fI2\.0\fR)\.
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
.RE
.PP
\fB\-I\fR
.RS 4
-Insertion pseudocount (\fI0\.02\fR)\.
+Insertion pseudocount (\fI0\&.02\fR)\&.
.RE
.PP
\fB\-J\fR
.RS 4
-No\-insertion pseudocount (\fI1\.0\fR)\.
+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)\.
+Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\&.
.RE
.PP
\fB\-t\fR
.RS 4
-Initial temperature (\fI1\.2\fR)\.
+Initial temperature (\fI1\&.2\fR)\&.
.RE
.PP
\fB\-c\fR
.RS 4
-Cooling factor per n iterations (\fI1\.44\fR)\.
+Cooling factor per n iterations (\fI1\&.44\fR)\&.
.RE
.PP
\fB\-u\fR
.RS 4
-Temperature lower bound (\fI0\.1\fR)\.
+Temperature lower bound (\fI0\&.1\fR)\&.
.RE
.PP
\fB\-p\fR
.RS 4
-Print progress information at each iteration\.
+Print progress information at each iteration\&.
.RE
.PP
\fB\-m\fR
.RS 4
-Column\-sampling moves per site\-sampling move (\fI1\.0\fR)\.
+Column\-sampling moves per site\-sampling move (\fI1\&.0\fR)\&.
.RE
.PP
\fB\-x\fR
@@ -131,12 +131,12 @@
Site sampling algorithm:
\fI0\fR=FAST
\fI1\fR=SLOW
-\fI2\fR=FFT (\fI0\fR)\.
+\fI2\fR=FFT (\fI0\fR)\&.
.RE
.PP
\fB\-s\fR
.RS 4
-Seed for pseudo\-random numbers (\fI1\fR)\.
+Seed for pseudo\-random numbers (\fI1\fR)\&.
.RE
.SH "SEE ALSO"
.PP
@@ -146,29 +146,29 @@
\fBglam2scan\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
-\fIhttp://bioinformatics\.org\.au/glam2/\fR
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
-\fI/usr/share/doc/glam2/\fR\.
+\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)\.
+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\.
+Author of GLAM2\&.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2\.
+Author of GLAM2\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Formatted this manpage in DocBook XML for the Debian distribution\.
+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\.
+The source code and the documentation of GLAM2 are released in the public domain\&.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1.xml 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2.1.xml 2008-05-18 09:51:09 UTC (rev 1887)
@@ -14,7 +14,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
Modified: trunk/packages/glam2/trunk/debian/glam2format.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2format.1 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,53 +1,53 @@
.\" Title: GLAM2FORMAT
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/26/2008
+.\" Date: 05/19/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2FORMAT" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.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
+glam2format \- converts GLAM2 motifs to FASTA or MSF format
.SH "SYNOPSIS"
.HP 12
-\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\.glam2\fR
+\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\&.glam2\fR
.PP
-Formats: fasta, msf\.
+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, 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\.
+output is converted\&.
.SH "OPTIONS (DEFAULT SETTINGS)"
.PP
\fB\-o\fR
.RS 4
-Output file (\fIstdout\fR)\.
+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
+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\.
+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
+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\.
+option\&. The sequences should have unique names and their order should be unchanged\&.
.RE
.SH "SEE ALSO"
.PP
@@ -58,29 +58,29 @@
\fBglam2scan\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
-\fIhttp://bioinformatics\.org\.au/glam2/\fR
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
-\fI/usr/share/doc/glam2/\fR\.
+\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)\.
+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\.
+Author of GLAM2\&.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2\.
+Author of GLAM2\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Formatted this manpage in DocBook XML for the Debian distribution\.
+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\.
+The source code and the documentation of GLAM2 are released in the public domain\&.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2format.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1.xml 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2format.1.xml 2008-05-18 09:51:09 UTC (rev 1887)
@@ -14,7 +14,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
Modified: trunk/packages/glam2/trunk/debian/glam2mask.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2mask.1 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2mask.1 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,41 +1,41 @@
.\" Title: GLAM2MASK
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/26/2008
+.\" Date: 05/19/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2MASK" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.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
+glam2mask \- masks a GLAM2 motif in sequences
.SH "SYNOPSIS"
.HP 10
-\fBglam2mask\fR [\fBoptions\fR] \fImy_motif\.glam2\fR \fImy_seqs\.fa\fR
+\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
+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\.
+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)\.
+Output file (\fIstdout\fR)\&.
.RE
.PP
\fB\-x\fR
.RS 4
-Mask character (\fIx\fR)\.
+Mask character (\fIx\fR)\&.
.RE
.SH "SEE ALSO"
.PP
@@ -45,29 +45,29 @@
\fBglam2scan\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
-\fIhttp://bioinformatics\.org\.au/glam2/\fR
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
-\fI/usr/share/doc/glam2/\fR\.
+\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)\.
+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\.
+Author of GLAM2\&.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2\.
+Author of GLAM2\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Formatted this manpage in DocBook XML for the Debian distribution\.
+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\.
+The source code and the documentation of GLAM2 are released in the public domain\&.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2mask.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2mask.1.xml 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2mask.1.xml 2008-05-18 09:51:09 UTC (rev 1887)
@@ -14,7 +14,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
Modified: trunk/packages/glam2/trunk/debian/glam2scan.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,77 +1,77 @@
.\" Title: GLAM2SCAN
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/26/2008
+.\" Date: 05/19/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2SCAN" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.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
+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
+\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\.
+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\.
+\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\.
+Show all options and their default settings\&.
.RE
.PP
\fB\-o\fR
.RS 4
-Output file (\fIstdout\fR)\.
+Output file (\fIstdout\fR)\&.
.RE
.PP
\fB\-n\fR
.RS 4
-Number of alignments to report (\fI25\fR)\.
+Number of alignments to report (\fI25\fR)\&.
.RE
.PP
\fB\-2\fR
.RS 4
-Examine both strands \- forward and reverse complement\.
+Examine both strands \- forward and reverse complement\&.
.RE
.PP
\fB\-D\fR
.RS 4
-Deletion pseudocount (\fI0\.1\fR)\.
+Deletion pseudocount (\fI0\&.1\fR)\&.
.RE
.PP
\fB\-E\fR
.RS 4
-No\-deletion pseudocount (\fI2\.0\fR)\.
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
.RE
.PP
\fB\-I\fR
.RS 4
-Insertion pseudocount (\fI0\.02\fR)\.
+Insertion pseudocount (\fI0\&.02\fR)\&.
.RE
.PP
\fB\-J\fR
.RS 4
-No\-insertion pseudocount (\fI1\.0\fR)\.
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
.RE
.PP
\fB\-d\fR
.RS 4
-Dirichlet mixture file\.
+Dirichlet mixture file\&.
.RE
.SH "SEE ALSO"
.PP
@@ -81,29 +81,29 @@
\fBglam2\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
-\fIhttp://bioinformatics\.org\.au/glam2/\fR
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
-\fI/usr/share/doc/glam2/\fR\.
+\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)\.
+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\.
+Author of GLAM2\&.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2\.
+Author of GLAM2\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Formatted this manpage in DocBook XML for the Debian distribution\.
+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\.
+The source code and the documentation of GLAM2 are released in the public domain\&.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2scan.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1.xml 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1.xml 2008-05-18 09:51:09 UTC (rev 1887)
@@ -14,7 +14,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
Modified: trunk/packages/glam2/trunk/debian/install
===================================================================
--- trunk/packages/glam2/trunk/debian/install 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/install 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,5 +1,5 @@
src/glam2format /usr/bin/
src/glam2mask /usr/bin/
src/glam2scan /usr/bin/
-src/glam2 /usr/bin/
-purge/glam2-purge /usr/bin
+src/glam2fft /usr/bin/
+purge/purge /usr/bin
Added: trunk/packages/glam2/trunk/debian/patches/CFLAGS-support.patch
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/CFLAGS-support.patch (rev 0)
+++ trunk/packages/glam2/trunk/debian/patches/CFLAGS-support.patch 2008-05-18 09:51:09 UTC (rev 1887)
@@ -0,0 +1,53 @@
+Description: Introduces support for the CFLAGS variables in glam2's Makefiles,
+ so that the Debian building system can modify the optimisation levels.
+Author: Charles Plessy <plessy at debian.org>
+Forwared: Not yet
+--- a/purge/Makefile
++++ b/purge/Makefile
+@@ -1,3 +1,4 @@
+ # Command for compiling purge:
++CFLAGS = -Wall -O3
+ purge: *.c *.h Makefile
+- cc -Wall -O3 -o purge *.c -lm
++ cc $(CFLAGS) -o purge *.c -lm
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,6 +6,7 @@
+ # -Wall means turn on compiler warnings (optional)
+ # -O3 means optimization level 3 (the maximum for gcc)
+ # -lm means include the math library
++CFLAGS = -Wall -O3
+
+ # Source files for glam2:
+ GSRC = alphabet.c args.c column_sample.c dirichlet.c dna_prior.c \
+@@ -28,25 +29,25 @@
+
+ # Command for compiling glam2:
+ glam2: $(GSRC) *.h Makefile
+- cc -Wall -O3 -o glam2 $(GSRC) -lm
++ cc $(CFLAGS) -o glam2 $(GSRC) -lm
+
+ # Command for compiling glam2scan:
+ glam2scan: $(SSRC) *.h Makefile
+- cc -Wall -O3 -o glam2scan $(SSRC) -lm
++ cc $(CFLAGS) -o glam2scan $(SSRC) -lm
+
+ # Command for compiling glam2format:
+ glam2format: $(FSRC) *.h Makefile
+- cc -Wall -O3 -o glam2format $(FSRC) -lm
++ cc $(CFLAGS) -o glam2format $(FSRC) -lm
+
+ # Command for compiling glam2mask:
+ glam2mask: $(MSRC) *.h Makefile
+- cc -Wall -O3 -o glam2mask $(MSRC) -lm
++ cc $(CFLAGS) -o glam2mask $(MSRC) -lm
+
+ # Here follow commands for compiling special versions of the programs
+
+ # Compile glam2 including FFT algorithm (requires FFTW to be installed):
+ glam2fft: $(GSRC) convolve.c *.h Makefile
+- cc -Wall -O3 -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3
++ cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3
+
+ # Compile for debugging with gdb or valgrind, with extra compiler warnings:
+ glam2_d: $(GSRC) *.h Makefile
Deleted: trunk/packages/glam2/trunk/debian/patches/Makefiles
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/Makefiles 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/patches/Makefiles 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,66 +0,0 @@
---- a/purge/Makefile
-+++ b/purge/Makefile
-@@ -1,3 +1,5 @@
- # Command for compiling purge:
--purge: *.c *.h Makefile
-- cc -Wall -O3 -o purge *.c -lm
-+# Renamed glam2-purge in Debian
-+CFLAGS = -g -Wall -O2
-+glam2-purge: *.c *.h Makefile
-+ cc $(CFLAGS) -o glam2-purge *.c -lm
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -6,6 +6,8 @@
- # -Wall means turn on compiler warnings (optional)
- # -O3 means optimization level 3 (the maximum for gcc)
- # -lm means include the math library
-+# In Debian, optimisation level can be overriden by build options.
-+CFLAGS = -g -Wall -O2
-
- # Source files for glam2:
- GSRC = alphabet.c args.c column_sample.c dirichlet.c dna_prior.c \
-@@ -27,26 +29,28 @@
- all: glam2 glam2scan glam2format glam2mask
-
- # Command for compiling glam2:
--glam2: $(GSRC) *.h Makefile
-- cc -Wall -O3 -o glam2 $(GSRC) -lm
-+# The Debian package uses an fft-enabled version of glam2.
-+glam2nofft: $(GSRC) *.h Makefile
-+ cc $(CFLAGS) -o glam2nofft $(GSRC) -lm
-
- # Command for compiling glam2scan:
- glam2scan: $(SSRC) *.h Makefile
-- cc -Wall -O3 -o glam2scan $(SSRC) -lm
-+ cc $(CFLAGS) -o glam2scan $(SSRC) -lm
-
- # Command for compiling glam2format:
- glam2format: $(FSRC) *.h Makefile
-- cc -Wall -O3 -o glam2format $(FSRC) -lm
-+ cc $(CFLAGS) -o glam2format $(FSRC) -lm
-
- # Command for compiling glam2mask:
- glam2mask: $(MSRC) *.h Makefile
-- cc -Wall -O3 -o glam2mask $(MSRC) -lm
-+ cc $(CFLAGS) -o glam2mask $(MSRC) -lm
-
- # Here follow commands for compiling special versions of the programs
-
- # Compile glam2 including FFT algorithm (requires FFTW to be installed):
--glam2fft: $(GSRC) convolve.c *.h Makefile
-- cc -Wall -O3 -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3
-+# glam2fft is simply renamed glam2 in Debian.
-+glam2: $(GSRC) convolve.c *.h Makefile
-+ cc $(CFLAGS) -DFFT -o glam2 $(GSRC) convolve.c -lm -lfftw3
-
- # Compile for debugging with gdb or valgrind, with extra compiler warnings:
- glam2_d: $(GSRC) *.h Makefile
---- /dev/null
-+++ b/Makefile
-@@ -0,0 +1,6 @@
-+all:
-+ make -C src all
-+ make -C purge
-+
-+clean:
-+ rm -f purge/*.o purge/purge purge/glam2-purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan,glam2fft}
Modified: trunk/packages/glam2/trunk/debian/patches/series
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/series 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/patches/series 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1 +1 @@
-Makefiles
+CFLAGS-support.patch
Modified: trunk/packages/glam2/trunk/debian/rules
===================================================================
--- trunk/packages/glam2/trunk/debian/rules 2008-05-18 07:01:06 UTC (rev 1886)
+++ trunk/packages/glam2/trunk/debian/rules 2008-05-18 09:51:09 UTC (rev 1887)
@@ -1,10 +1,27 @@
#!/usr/bin/make -f
-DEB_COMPRESS_EXCLUDE := .pdf
+DEB_COMPRESS_EXCLUDE := .pdf # The PDF doc will not be compressed
include /usr/share/cdbs/1/rules/patchsys-quilt.mk
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/makefile.mk
-DEB_MAKE_BUILD_TARGET = all
-DEB_MAKE_CLEAN_TARGET = clean
+DEB_MAKE_BUILD_TARGET = --directory src all glam2fft
+build/glam2::
+ $(DEB_MAKE_INVOKE) --directory purge
+
+BINDIR = $(CURDIR)/debian/glam2/usr/bin
+binary-fixup/glam2::
+ # purge is renamed glam2-purge to avoid namespace problems.
+ mv $(BINDIR)/purge $(BINDIR)/glam2-purge
+ # FFT is enabled by default in Debian.
+ mv $(BINDIR)/glam2fft $(BINDIR)/glam2
+
+clean::
+ rm -f purge/*.o purge/purge src/*.o src/glam2, src/glam2mask, scr/glam2format src/glam2scan src/glam2fft
+
+get-orig-source:
+ # The unzip command from the unzip package is needed for this one.
+ [ -f ../glam2-$(DEB_UPSTREAM_VERSION).zip ] || uscan --force-download
+ unzip ../glam2-$(DEB_UPSTREAM_VERSION).zip -d..
+ tar --create --gzip --file ../glam2_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../glam2-$(DEB_UPSTREAM_VERSION)
More information about the debian-med-commit
mailing list