[med-svn] r4850 - trunk/packages/beast-mcmc/trunk/debian
Felix Feyertag
fxf-guest at alioth.debian.org
Fri May 28 15:47:48 UTC 2010
Author: fxf-guest
Date: 2010-05-28 15:47:43 +0000 (Fri, 28 May 2010)
New Revision: 4850
Removed:
trunk/packages/beast-mcmc/trunk/debian/menu
Modified:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
trunk/packages/beast-mcmc/trunk/debian/beauti.1
Log:
Update man pages and add menu item.
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1 2010-05-27 23:36:52 UTC (rev 4849)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1 2010-05-28 15:47:43 UTC (rev 4850)
@@ -1,29 +1,21 @@
-'\" t
.\" Title: BEAST-MCMC
.\" Author: Alexei J. Drummond
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 01/19/2010
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/28/2010
.\" Manual: BEAST-MCMC Manual
.\" Source: BEAST 1.5.3
-.\" Language: English
.\"
-.TH "BEAST\-MCMC" "1" "01/19/2010" "BEAST 1.5.3" "BEAST-MCMC Manual"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
+.TH "BEAST\-MCMC" "1" "05/28/2010" "BEAST 1.5.3" "BEAST-MCMC Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
.SH "NAME"
beast-mcmc \- Bayesian evolutionary analysis sampling trees
.SH "SYNOPSIS"
-.HP \w'\fBbeast\-mcmc\fR\ 'u
+.HP 11
\fBbeast\-mcmc\fR [\fBOPTIONS\fR] [\fIinput\&.xml\fR]
-.HP \w'\fBbeast\-mcmc\fR\ 'u
+.HP 11
\fBbeast\-mcmc\fR [\fB\-verbose\fR | \fB\-strict\fR | \fB\-window\fR | \fB\-options\fR | \fB\-working\fR | \fB\-seed\fR | \fB\-errors\ i\fR | \fB\-threads\ i\fR | \fB\-java\fR | \fB\-beagle\fR | \fB\-beagle_info\fR | \fB\-beagle_resource_order\fR | \fB\-help\fR | \fBinput\&.xml\fR]
.SH "DESCRIPTION"
.PP
@@ -97,82 +89,53 @@
.SH "BUGS"
.PP
The BEAST bug tracking system can be found at
-\m[blue]\fB\%http://code.google.com/p/beast-mcmc/issues/list\fR\m[]\&.
+\fI\%http://code.google.com/p/beast-mcmc/issues/list\fR\&.
.SH "SEE ALSO"
.PP
\fBbeauti\fR(1)\&.
.SH "REFERENCES"
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&.
.RE
.SH "AUTHORS"
.PP
\fBAlexei J\&. Drummond\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAST\&.
-.RE
.PP
\fBAndrew Rambaut\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAST\&.
-.RE
.PP
\fBMarc A\&. Suchard\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAST\&.
-.RE
.PP
\fBFelix Feyertag\fR <\&felix\&.feyertag at googlemail\&.com\&>
-.RS 4
+.sp -1n
+.IP "" 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
-.RE
.SH "COPYRIGHT"
+Copyright \(co 2002\(en2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)
.br
-CopyrightCopyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)
+Copyright \(co 2009\(en2010 Felix Feyertag (This manpage)
.br
-Copyright \(co 2002\(en2009 Felix Feyertag (This manpage)
-.br
.PP
The binaries and source code are made available and can be distributed subject to the following conditions:
.PP
@@ -181,47 +144,19 @@
BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&.
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
+\h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
+\h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
+\h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
+\h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
.RE
.PP
This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2010-05-27 23:36:52 UTC (rev 4849)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2010-05-28 15:47:43 UTC (rev 4850)
@@ -1,28 +1,12 @@
-?package(beast-mcmc):
- needs="text"\
- section="Applications/Science/Biology"\
- title="BEAST"\
- command="/usr/bin/beast-mcmc"\
- hints="Bayesian evolutionary analysis sampling trees"\
- icon="/usr/share/pixmaps/beast.png"
-
?package(beast-mcmc):\
needs="x11"\
section="Applications/Science/Biology"\
title="BEAST"\
- command="/usr/bin/beast-mcmc"\
+ command="xterm -e bash -c \"/usr/bin/beast-mcmc; read\""\
hints="Bayesian evolutionary analysis sampling trees"\
icon="/usr/share/pixmaps/beast.png"
?package(beast-mcmc):\
- needs="text"\
- section="Applications/Science/Biology"\
- title="BEAUti"\
- command="/usr/bin/beauti"\
- hints="Bayesian Evolutionary Analysis Utility"\
- icon="/usr/share/pixmaps/beast.png"
-
-?package(beast-mcmc):\
needs="x11"\
section="Applications/Science/Biology"\
title="BEAUti"\
Modified: trunk/packages/beast-mcmc/trunk/debian/beauti.1
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beauti.1 2010-05-27 23:36:52 UTC (rev 4849)
+++ trunk/packages/beast-mcmc/trunk/debian/beauti.1 2010-05-28 15:47:43 UTC (rev 4850)
@@ -1,27 +1,19 @@
-'\" t
.\" Title: BEAUTI
.\" Author: Alexei J. Drummond
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 01/19/2010
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 05/28/2010
.\" Manual: BEAUti Manual
.\" Source: BEAUti 1.5.3
-.\" Language: English
.\"
-.TH "BEAUTI" "1" "01/19/2010" "BEAUti 1.5.3" "BEAUti Manual"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
+.TH "BEAUTI" "1" "05/28/2010" "BEAUti 1.5.3" "BEAUti Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
.SH "NAME"
beauti \- Bayesian Evolutionary Analysis Utility
.SH "SYNOPSIS"
-.HP \w'\fBbeauti\fR\ 'u
+.HP 7
\fBbeauti\fR [\fInexus_file\ template_file\ beast_file\fR]
.SH "DESCRIPTION"
.PP
@@ -29,80 +21,51 @@
.SH "BUGS"
.PP
The BEAUti bug tracking system can be found at
-\m[blue]\fB\%http://code.google.com/p/beast-mcmc/issues/list\fR\m[]\&.
+\fI\%http://code.google.com/p/beast-mcmc/issues/list\fR\&.
.SH "SEE ALSO"
.PP
\fBbeast-mcmc\fR(1)\&.
.SH "REFERENCES"
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&.
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&.
+\h'-04'\(bu\h'+03'Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&.
.RE
.SH "AUTHORS"
.PP
\fBAlexei J\&. Drummond\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAUti\&.
-.RE
.PP
\fBAndrew Rambaut\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAUti\&.
-.RE
.PP
\fBMarc A\&. Suchard\fR
-.RS 4
+.sp -1n
+.IP "" 4
Copyright holder for BEAUti\&.
-.RE
.PP
\fBFelix Feyertag\fR <\&felix\&.feyertag at googlemail\&.com\&>
-.RS 4
+.sp -1n
+.IP "" 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
-.RE
.SH "COPYRIGHT"
+Copyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAUti)
.br
-CopyrightCopyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAUti)
-.br
Copyright \(co 2002\(en2009 Felix Feyertag (This manpage)
.br
.PP
@@ -113,47 +76,19 @@
BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&.
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
+\h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
+\h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
+\h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
.RE
.sp
.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
+\h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
.RE
.PP
This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
Deleted: trunk/packages/beast-mcmc/trunk/debian/menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/menu 2010-05-27 23:36:52 UTC (rev 4849)
+++ trunk/packages/beast-mcmc/trunk/debian/menu 2010-05-28 15:47:43 UTC (rev 4850)
@@ -1,8 +0,0 @@
-?package(beast-mcmc):\
-needs="X11"\
-section="Applications/Science/Biology"\
-title="BEAST"\
-command="/usr/bin/beast-mcmc"\
-icon="/usr/share/pixmaps/beast.png" \
-hints="Phylogenetic inference"\
-longtitle="BEAST: Bayesian MCMC phylogenetic inference"
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