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\&.feyer...@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\&.feyer...@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" _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
