[med-svn] r835 - trunk/packages/probcons/trunk/debian
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Sun Nov 18 11:01:43 UTC 2007
Author: hanska-guest
Date: 2007-11-18 11:01:43 +0000 (Sun, 18 Nov 2007)
New Revision: 835
Added:
trunk/packages/probcons/trunk/debian/pc-compare.1
trunk/packages/probcons/trunk/debian/pc-makegnuplot.1
trunk/packages/probcons/trunk/debian/pc-project.1
trunk/packages/probcons/trunk/debian/probcons-RNA.1
trunk/packages/probcons/trunk/debian/probcons.1
Modified:
trunk/packages/probcons/trunk/debian/changelog
trunk/packages/probcons/trunk/debian/control
trunk/packages/probcons/trunk/debian/rules
Log:
* debian/probcons.1, debian/probcons-RNA.1, debian/pc-compare.1,
debian/pc-makegnuplot.1, debian/pc-project.1 added - these
have been statically built.
* debian/control:
- B-D updated
- added myself to Uploaders
* debian/rules:
- manpages statically built
- minor changes
Modified: trunk/packages/probcons/trunk/debian/changelog
===================================================================
--- trunk/packages/probcons/trunk/debian/changelog 2007-11-18 10:55:51 UTC (rev 834)
+++ trunk/packages/probcons/trunk/debian/changelog 2007-11-18 11:01:43 UTC (rev 835)
@@ -1,9 +1,21 @@
-probcons (1.12-4) unreleased; urgency=low
+probcons (1.12-4) UNRELEASED; urgency=low
+ [ Charles Plessy ]
* Moved the Homepage: field out from the package's description.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 21 Sep 2007 23:22:08 +0900
+ [ David Paleino ]
+ * debian/probcons.1, debian/probcons-RNA.1, debian/pc-compare.1,
+ debian/pc-makegnuplot.1, debian/pc-project.1 added - these
+ have been statically built.
+ * debian/control:
+ - B-D updated
+ - added myself to Uploaders
+ * debian/rules:
+ - manpages statically built
+ - minor changes
+ -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 11:59:43 +0100
+
probcons (1.12-3) unstable; urgency=low
* Fixed typos which caused incomplete cleaning (Closes: #424301).
Modified: trunk/packages/probcons/trunk/debian/control
===================================================================
--- trunk/packages/probcons/trunk/debian/control 2007-11-18 10:55:51 UTC (rev 834)
+++ trunk/packages/probcons/trunk/debian/control 2007-11-18 11:01:43 UTC (rev 835)
@@ -2,8 +2,9 @@
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), xsltproc, docbook-xml, docbook-xsl, dpatch
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5), dpatch
Standards-Version: 3.7.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/probcons/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/probcons
Added: trunk/packages/probcons/trunk/debian/pc-compare.1
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-compare.1 (rev 0)
+++ trunk/packages/probcons/trunk/debian/pc-compare.1 2007-11-18 11:01:43 UTC (rev 835)
@@ -0,0 +1,49 @@
+.\" Title: PC-COMPARE
+.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2007-04-04
+.\" Manual: Probcons Manual
+.\" Source: pc-compare 1.12
+.\"
+.TH "PC\-COMPARE" "1" "2007\-04\-04" "pc-compare 1.12" "Probcons Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores.
+.SH "SYNOPSIS"
+.HP 11
+\fBpc\-compare\fR [\fITEST_ALIGNMENT\fR] [\fIREFERENCE_ALIGNMENT\fR] [\fIBALIBASE_ANNOT_FILE\fR] [\fB\-col\fR] [\fB\-core\fR] [\fB\-caps\fR] [\fB\-annot\ \fR\fB\fIFILENAME\fR\fR]
+.SH "NOTE"
+.PP
+pc\-compare is named
+\fIcompare\fR
+in the original sources, but has been remamed to avoid collision with other program names\.
+.SH "SEE ALSO"
+.PP
+
+\fBpc-makegnufile\fR(1),
+\fBpc-project\fR(1),from the probcons\-extra package, and
+\fBprobcons\fR(1)
+and
+\fBprobcons-RNA\fR(1)
+from the probcons package\.
+.SH "REFERENCE"
+.PP
+Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+.SH "AUTHORS"
+.PP
+\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
+.sp -1n
+.IP "" 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+This program and its manpage are in the public domain\.
+.sp
Added: trunk/packages/probcons/trunk/debian/pc-makegnuplot.1
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-makegnuplot.1 (rev 0)
+++ trunk/packages/probcons/trunk/debian/pc-makegnuplot.1 2007-11-18 11:01:43 UTC (rev 835)
@@ -0,0 +1,49 @@
+.\" Title: PC-MAKEGNUPLOT
+.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2007-04-04
+.\" Manual: Probcons Manual
+.\" Source: pc-makegnuplot 1.12
+.\"
+.TH "PC\-MAKEGNUPLOT" "1" "2007\-04\-04" "pc-makegnuplot 1.12" "Probcons Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+pc-makegnuplot - Utility to plot annotation scores.
+.SH "SYNOPSIS"
+.HP 15
+\fBpc\-makegnuplot\fR [\fIannotscores\fR] [\-refscores]
+.SH "NOTE"
+.PP
+pc\-makegnuplot is named
+\fImakegnuplot\fR
+in the original sources, but has been remamed to avoid collision with other program names\.
+.SH "SEE ALSO"
+.PP
+
+\fBpc-compare\fR(1),
+\fBpc-project\fR(1),from the probcons\-extra package, and
+\fBprobcons\fR(1)
+and
+\fBprobcons-RNA\fR(1)
+from the probcons package\.
+.SH "REFERENCE"
+.PP
+Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+.SH "AUTHORS"
+.PP
+\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
+.sp -1n
+.IP "" 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+This program and its manpage are in the public domain\.
+.sp
Added: trunk/packages/probcons/trunk/debian/pc-project.1
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-project.1 (rev 0)
+++ trunk/packages/probcons/trunk/debian/pc-project.1 2007-11-18 11:01:43 UTC (rev 835)
@@ -0,0 +1,49 @@
+.\" Title: PC-PROJECT
+.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2007-04-04
+.\" Manual: Probcons Manual
+.\" Source: pc-project 1.12
+.\"
+.TH "PC\-PROJECT" "1" "2007\-04\-04" "pc-project 1.12" "Probcons Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+pc-project - Program to project multiple alignment to pairwise alignments.
+.SH "SYNOPSIS"
+.HP 11
+\fBpc\-project\fR [\fIALIGNMENT\fR] [\-nocompressgaps]
+.SH "NOTE"
+.PP
+pc\-project is named
+\fIproject\fR
+in the original sources, but has been remamed to avoid collision with other program names\.
+.SH "SEE ALSO"
+.PP
+
+\fBpc-makegnufile\fR(1),
+\fBpc-compare\fR(1),from the probcons\-extra package, and
+\fBprobcons\fR(1)
+and
+\fBprobcons-RNA\fR(1)
+from the probcons package\.
+.SH "REFERENCE"
+.PP
+Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+.SH "AUTHORS"
+.PP
+\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
+.sp -1n
+.IP "" 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+This program and its manpage are in the public domain\.
+.sp
Added: trunk/packages/probcons/trunk/debian/probcons-RNA.1
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-RNA.1 (rev 0)
+++ trunk/packages/probcons/trunk/debian/probcons-RNA.1 2007-11-18 11:01:43 UTC (rev 835)
@@ -0,0 +1,51 @@
+.\" Title: PROBCONS-RNA
+.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2007-04-04
+.\" Manual: Probcons Manual
+.\" Source: probcons-RNA 1.12
+.\"
+.TH "PROBCONS\-RNA" "1" "2007\-04\-04" "probcons-RNA 1.12" "Probcons Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+probcons-RNA - An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE.
+.SH "DESCRIPTION"
+.PP
+See the manpage of
+\fBprobcons\fR(1)
+for the command\-line arguments, and
+\fI/usr/share/doc/README\.Debian\fR
+for more informations about how probcons\-RNA has been built\.
+.SH "SEE ALSO"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in
+\fI/usr/share/doc/probcons/manual\.pdf\fR
+in Debian systems\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'
+\fBprobcons\fR(1),
+\fBpc-makegnufile\fR(1),
+\fBpc-compare\fR(1),
+\fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\.
+.RE
+.SH "AUTHORS"
+.PP
+\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
+.sp -1n
+.IP "" 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+This program and its manpage are in the public domain\.
+.sp
Added: trunk/packages/probcons/trunk/debian/probcons.1
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.1 (rev 0)
+++ trunk/packages/probcons/trunk/debian/probcons.1 2007-11-18 11:01:43 UTC (rev 835)
@@ -0,0 +1,134 @@
+.\" Title: PROBCONS
+.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2007-04-04
+.\" Manual: Probcons Manual
+.\" Source: probcons 1.12
+.\"
+.TH "PROBCONS" "1" "2007\-04\-04" "probcons 1.12" "Probcons Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+probcons - align multiple protein sequences and print to standard output
+.SH "SYNOPSIS"
+.HP 9
+\fBprobcons\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR]
+.SH "DESCRIPTION"
+.PP
+\fBprobcons\fR
+is a tool for generating multiple alignments of protein sequences\. Using a combination of probabilistic modeling and consistency\-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date\. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T\-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN\.
+.PP
+\fBprobcons\fR
+aligns sequences provided in MFA format\. This format consists of multiple sequences\. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\. The description line is distinguished from the sequence data by a greater\-than (\(lq>\(rq) symbol in the first column\.
+.SH "OPTIONS"
+.PP
+\fB\-clustalw\fR
+.RS 4
+use CLUSTALW output format instead of MFA
+.RE
+.PP
+\fB\-c\fR \fB\-\-consistency\fR \fIREPS\fR
+.RS 4
+use 0 <=
+\fIREPS\fR
+<= 5 (default: 2) passes of consistency transformation
+.RE
+.PP
+\fB\-ir\fR \fB\-\-iterative\-refinement\fR \fIREPS\fR
+.RS 4
+use 0 <=
+\fIREPS\fR
+<=1000 (default: 100) passes of iterative\-refinement
+.RE
+.PP
+\fB\-pre\fR \fB\-\-pre\-training\fR \fIREPS\fR
+.RS 4
+use 0 <=
+\fIREPS\fR
+<= 20 (default: 0) rounds of pretraining
+.RE
+.PP
+\fB\-pairs\fR
+.RS 4
+generate all\-pairs pairwise alignments
+.RE
+.PP
+\fB\-viterbi\fR
+.RS 4
+use Viterbi algorithm to generate all pairs (automatically enables
+\fB\-pairs\fR)
+.RE
+.PP
+\fB\-v\fR \fB\-\-verbose\fR
+.RS 4
+Report progress while aligning (default: off)
+.RE
+.PP
+\fB\-annot\fR \fIFILENAME\fR
+.RS 4
+write annotation for multiple alignment to
+\fIFILENAME\fR
+.RE
+.PP
+\fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR
+.RS 4
+compute EM transition probabilities, store in
+\fIFILENAME\fR
+(default: no training)
+.RE
+.PP
+\fB\-e\fR \fB\-\-emissions\fR
+.RS 4
+also reestimate emission probabilities (default: off)
+.RE
+.PP
+\fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR
+.RS 4
+read parameters from
+\fIFILENAME\fR
+(default: )
+.RE
+.PP
+\fB\-a\fR \fB\-\-alignment\-order\fR
+.RS 4
+print sequences in alignment order rather than input order (default: off)
+.RE
+.SH "SEE ALSO"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in
+\fI/usr/share/doc/probcons/manual\.pdf\fR
+in Debian systems\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE,
+\fBprobcons-RNA\fR(1), is also distributed in the ProbCons Debian package\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'
+\fBpc-makegnufile\fR(1),
+\fBpc-compare\fR(1),
+\fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\.
+.RE
+.SH "REFERENCE"
+.PP
+Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+.SH "AUTHORS"
+.PP
+\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
+.sp -1n
+.IP "" 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+This program and its manpage are in the public domain\.
+.sp
Modified: trunk/packages/probcons/trunk/debian/rules
===================================================================
--- trunk/packages/probcons/trunk/debian/rules 2007-11-18 10:55:51 UTC (rev 834)
+++ trunk/packages/probcons/trunk/debian/rules 2007-11-18 11:01:43 UTC (rev 835)
@@ -9,12 +9,12 @@
# be used without restriction.
BINARIES = probcons probcons-RNA pc-project pc-compare pc-makegnuplot
-MANPAGES = probcons.1 probcons-RNA.1 pc-compare.1 pc-project.1 pc-makegnuplot.1
XP = xsltproc \
-''-nonet \
-''-param man.charmap.use.subset "0" \
-''-param make.year.ranges "1" \
- -''-param make.single.year.ranges "1"
+ -''-param make.single.year.ranges "1" \
+ -o debian/
CFLAGS = -Wall -g
@@ -26,30 +26,25 @@
include /usr/share/dpatch/dpatch.make
-build: patch build-stamp manpages
-
+build: patch build-stamp
build-stamp:
dh_testdir
cp Main.cc Main-RNA.cc
cp debian/Defaults-RNA.h Defaults-RNA.h
$(MAKE)
- touch build-stamp
+ touch $@
-manpages: manpages-stamp
-
-manpages-stamp: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/pc-project.1.xml debian/pc-compare.1.xml debian/pc-makegnuplot.1.xml
+manpages: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/pc-project.1.xml debian/pc-compare.1.xml debian/pc-makegnuplot.1.xml
$(XP) debian/probcons.1.xml
$(XP) debian/probcons-RNA.1.xml
$(XP) debian/pc-project.1.xml
$(XP) debian/pc-compare.1.xml
$(XP) debian/pc-makegnuplot.1.xml
- touch manpages-stamp
clean: unpatch
dh_testdir
dh_testroot
- rm -f build-stamp manpages-stamp
- dh_clean $(BINARIES) $(MANPAGES) Main-RNA.cc Defaults-RNA.h
+ dh_clean $(BINARIES) Main-RNA.cc Defaults-RNA.h build-stamp
install: build
dh_testdir
@@ -59,7 +54,6 @@
ln -s probcons debian/probcons-extra/usr/share/doc/probcons-extra
binary-indep: build install
-
binary-arch: build install
dh_testdir
dh_testroot
More information about the debian-med-commit
mailing list