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 <[email protected]> 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
