[med-svn] [beast2-mcmc] 04/05: Wrote manpages

Wed May 4 11:34:57 UTC 2016

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository beast2-mcmc.

commit 45ca538d95225f86a285eddd1908f0ec1a5821b8
Author: Andreas Tille <tille at debian.org>
Date:   Wed May 4 13:13:18 2016 +0200

    Wrote manpages
---
 debian/manpages              |  1 +
 debian/mans/beast2-mcmc.1    | 82 ++++++++++++++++++++++++++++++++++++++++++++
 debian/mans/beauti2.1        | 42 +++++++++++++++++++++++
 debian/mans/treeannotator2.1 | 48 ++++++++++++++++++++++++++
 4 files changed, 173 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/beast2-mcmc.1 b/debian/mans/beast2-mcmc.1
new file mode 100644
index 0000000..f28ace4
--- /dev/null
+++ b/debian/mans/beast2-mcmc.1
@@ -0,0 +1,82 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BEAST2-MCMC "1" "May 2016" "beast2-mcmc 2.4.1" "User Commands"
+.SH NAME
+beast2-mcmc \- Bayesian MCMC phylogenetic inference
+.SH SYNOPSIS
+.B beast2-mcmc
+[\-window] [\-options] [\-working] [\-seed] [\-prefix <PREFIX>] [\-statefile <STATEFILE>] [\-overwrite] [\-resume] [\-validate] [\-errors <i>] [\-threads <i>] [\-java] [\-noerr] [\-loglevel <LEVEL>] [\-instances <i>] [\-beagle] [\-beagle_info] [\-beagle_order <order>] [\-beagle_CPU] [\-beagle_GPU] [\-beagle_SSE] [\-beagle_single] [\-beagle_double] [\-beagle_scaling <default|none|dynamic|always>] [\-help] [\-version] [<input\-file\-name>]
+.SH DESCRIPTION
+BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+sequences. It is entirely orientated towards rooted, time-measured
+phylogenies inferred using strict or relaxed molecular clock models. It
+can be used as a method of reconstructing phylogenies but is also a
+framework for testing evolutionary hypotheses without conditioning on a
+single tree topology. BEAST uses MCMC to average over tree space, so that
+each tree is weighted proportional to its posterior probability. Included
+is a simple to use user-interface program for setting up standard
+analyses and a suit of programs for analysing the results.
+.P
+This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
+version.
+.SH OPTIONS
+.HP
+\fB\-window\fR Provide a console window
+.HP
+\fB\-options\fR Display an options dialog
+.HP
+\fB\-working\fR Change working directory to input file's directory
+.HP
+\fB\-seed\fR Specify a random number generator seed
+.HP
+\fB\-prefix\fR Specify a prefix for all output log filenames
+.HP
+\fB\-statefile\fR Specify the filename for storing/restoring the state
+.HP
+\fB\-overwrite\fR Allow overwriting of log files
+.HP
+\fB\-resume\fR Allow appending of log files
+.HP
+\fB\-validate\fR Parse the XML, but do not run \fB\-\-\fR useful for debugging XML
+.HP
+\fB\-errors\fR Specify maximum number of numerical errors before stopping
+.HP
+\fB\-threads\fR The number of computational threads to use (default 1), \fB\-1\fR for number of cores
+.HP
+\fB\-java\fR Use Java only, no native implementations
+.HP
+\fB\-noerr\fR Suppress all output to standard error
+.HP
+\fB\-loglevel\fR error,warning,info,debug,trace
+.HP
+\fB\-instances\fR divide site patterns amongst number of threads (use with \fB\-threads\fR option)
+.HP
+\fB\-beagle\fR Use beagle library if available
+.HP
+\fB\-beagle_info\fR BEAGLE: show information on available resources
+.HP
+\fB\-beagle_order\fR BEAGLE: set order of resource use
+.HP
+\fB\-beagle_CPU\fR BEAGLE: use CPU instance
+.HP
+\fB\-beagle_GPU\fR BEAGLE: use GPU instance if available
+.HP
+\fB\-beagle_SSE\fR BEAGLE: use SSE extensions if available
+.HP
+\fB\-beagle_single\fR BEAGLE: use single precision if available
+.HP
+\fB\-beagle_double\fR BEAGLE: use double precision if available
+.HP
+\fB\-beagle_scaling\fR BEAGLE: specify scaling scheme to use
+.HP
+\fB\-help\fR Print this information and stop
+.HP
+\fB\-version\fR Print version and stop
+.SH EXAMPLES
+.IP
+beast2-mcmc test.xml
+.IP
+beast2-mcmc \fB\-window\fR test.xml
+.IP
+beast2-mcmc \fB\-help\fR
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/beauti2.1 b/debian/mans/beauti2.1
new file mode 100644
index 0000000..946ba35
--- /dev/null
+++ b/debian/mans/beauti2.1
@@ -0,0 +1,42 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BEAUTI2 "1" "May 2016" "beauti2 2.4.1" "User Commands"
+.SH NAME
+beauti2 \- matches beast2-mcmc
+.SH SYNOPSIS
+.B beauti2
+\fB\-template\fR [template file] \fB\-nex\fR [nexus data file] \fB\-xmldat\fR [beast xml file]
+\fB\-xml\fR [beast file] \fB\-exitaction\fR [writexml|usetemplate|usexml] \fB\-out\fR [output file name]
+\fB\-capture\fR \fB\-v\fR \fB\-version\fR \fB\-h\fR \fB\-help\fR
+.SH DESCRIPTION
+BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+sequences. It is entirely orientated towards rooted, time-measured
+phylogenies inferred using strict or relaxed molecular clock models. It
+can be used as a method of reconstructing phylogenies but is also a
+framework for testing evolutionary hypotheses without conditioning on a
+single tree topology. BEAST uses MCMC to average over tree space, so that
+each tree is weighted proportional to its posterior probability. Included
+is a simple to use user-interface program for setting up standard
+analyses and a suit of programs for analysing the results.
+.P
+This BEAUTI version matches BEAST2-MCMC.
+.SH OPTIONS
+.HP
+\fB\-template\fR [template file] : BEAUti template to be used. Default templates/Standard.xml
+.HP
+\fB\-nex\fR [nexus data file] : nexus file to be read using template, multiple \fB\-nex\fR arguments are allowed
+.HP
+\fB\-xmldat\fR [beast xml file] : as \fB\-nex\fR but with BEAST 1 or 2 xml file instead of nexus file
+.HP
+\fB\-xml\fR [beast file] : BEAST 2 XML file to be loaded
+.HP
+\fB\-exitaction\fR [writexml|usetemplate|usexml] : what to do after processing arguments
+.HP
+\fB\-out\fR [output file name] : file to be written
+.HP
+\fB\-capture\fR : captures stdout and stderr and make them available under Help/Messages menu
+.HP
+\fB\-v\fR, \fB\-version\fR : print version
+.HP
+\fB\-h\fR, \fB\-help\fR : print this help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/treeannotator2.1 b/debian/mans/treeannotator2.1
new file mode 100644
index 0000000..c610e8f
--- /dev/null
+++ b/debian/mans/treeannotator2.1
@@ -0,0 +1,48 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH TREEANNOTATOR2 "1" "May 2016" "treeannotator2 2.4.1" "User Commands"
+.SH NAME
+treeannotator2 \- MCMC Output analysis of beast2 package
+.SH SYNOPSIS
+.B treeannotator
+[\-heights <keep|median|mean|ca>] [\-burnin <i>] [\-b <i>] [\-limit <r>] [\-target <target_file_name>] [\-help] [\-forceDiscrete] [\-lowMem] [\-hpd2D <r>] <input\-file\-name> [<output\-file\-name>]
+.SH DESCRIPTION
+BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+sequences. It is entirely orientated towards rooted, time-measured
+phylogenies inferred using strict or relaxed molecular clock models. It
+can be used as a method of reconstructing phylogenies but is also a
+framework for testing evolutionary hypotheses without conditioning on a
+single tree topology. BEAST uses MCMC to average over tree space, so that
+each tree is weighted proportional to its posterior probability. Included
+is a simple to use user-interface program for setting up standard
+analyses and a suit of programs for analysing the results.
+.P
+This treeannotator version matches beast2-mcmc which is no new upstream version of beast-mcmc (1.x) but rather a rewritten
+version.
+.SH OPTIONS
+.HP
+\fB\-heights\fR an option of 'keep' (default), 'median', 'mean' or 'ca'
+.HP
+\fB\-burnin\fR the percentage of states to be considered as 'burn\-in'
+.HP
+\fB\-b\fR the percentage of states to be considered as 'burn\-in'
+.HP
+\fB\-limit\fR the minimum posterior probability for a node to be annotated
+.HP
+\fB\-target\fR specifies a user target tree to be annotated
+.HP
+\fB\-help\fR option to print this message
+.HP
+\fB\-forceDiscrete\fR forces integer traits to be treated as discrete traits.
+.HP
+\fB\-lowMem\fR use less memory, which is a bit slower.
+.HP
+\fB\-hpd2D\fR the HPD interval to be used for the bivariate traits
+.SH EXAMPLES
+.IP
+treeannotator2 test.trees out.txt
+.IP
+treeannotator2 \fB\-burnin\fR 10 \fB\-heights\fR mean test.trees out.txt
+.IP
+treeannotator2 \fB\-burnin\fR 20 \fB\-target\fR map.tree test.trees out.txt
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

-- 
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