[med-svn] [indelible] 01/04: Added patch with manpage

[Fabian Klötzl]

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kloetzl-guest pushed a commit to branch master
in repository indelible.

commit edd674c34933c1abaf9d774bd5abde64e1bf2191
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Sun Feb 7 15:40:33 2016 +0100

    Added patch with manpage
---
 debian/patches/0006-added-manpage.patch | 62 +++++++++++++++++++++++++++++++++
 debian/patches/series                   |  1 +
 2 files changed, 63 insertions(+)

diff --git a/debian/patches/0006-added-manpage.patch b/debian/patches/0006-added-manpage.patch
new file mode 100644
index 0000000..6ae12ea
--- /dev/null
+++ b/debian/patches/0006-added-manpage.patch
@@ -0,0 +1,62 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Sun, 7 Feb 2016 15:38:40 +0100
+Subject: added manpage
+
+---
+ indelible.1 | 47 +++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 47 insertions(+)
+ create mode 100644 indelible.1
+
+diff --git a/indelible.1 b/indelible.1
+new file mode 100644
+index 0000000..db525b7
+--- /dev/null
++++ b/indelible.1
+@@ -0,0 +1,47 @@
++.TH INDELIBLE "1" "2010" "1.03" ""
++.SH NAME
++indelible \- powerful and flexible simulator of biological evolution
++.SH SYNOPSIS
++.B indelible
++.TP
++No options can be passed via the commandline.
++.SH DESCRIPTION
++.TP
++\fBindelible\fR can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continous time. All common evolutionary models are supported.
++.TP
++The full documentation for \fBindelible\fR is available under \fI/usr/share/doc/indelible/help/index.html\fR.
++.SH CONFIGURATION
++.TP
++\fBindelible\fR reads the settings for a simulation run from a file named \fIcontrol.txt\fR in the current directory. The file is split into blocks, with each block controlling one particular aspect of the simulation. Blocks may contain further sub-blocks. Comments can be given in C or C++ style. If \fBindelible\fR is executed without a control file present, an example file is generated.
++.TP
++\fB[TYPE]\fR type
++Every control file must begin with a \fBTYPE\fR block. The possible types are \fINUCLEOTIDE\fR, \fIAMINOACID\fR, and \fICODON\fR.
++.TP
++\fB[SETTINGS]\fR
++This block specifies non-essential user preferences such as output file types and formats, seeds for the random number generator, and whether to output detailed reports.
++.TP
++\fB[MODEL]\fR modelname
++This block starts a new evolutionary model to be used for simulation. The particular parameters including substitution models, indel-rates and codon-site models are controlled via submodels. \fImodelname\fR can be any name of your choosing.
++.TP
++\fB[TREE]\fR treename newick
++This block is used to specify a guide-tree with the given name \fItreename\fR. Evolutionary distances are represented as branch lengths for the tree in \fINEWICK\fR format.
++.TP
++\fB[BRANCHES]\fR
++These blocks are used to simulate non-stationary and non-homogenous processes. Different models can be specified on different branches of the guide-tree allowing branches to have different models of substitution, indel length distribution, rate heterogeneity, base composition etc. 
++.TP
++\fB[PARTITIONS]\fR partitionname
++During each run multiple sequence partitions can be simulated. For each partition the guide-tree, evolutionary model and sequence length has to be specified.
++.TP
++\fB[EVOLVE]\fR
++Within this block multiple replicas of a partition may be generated.
++.SH COPYRIGHT
++Copyright \(co 2010 William Fletcher
++License GPLv3+: GNU GPL version 3 or later.
++.br
++This is free software: you are free to change and redistribute it.
++There is NO WARRANTY, to the extent permitted by law.
++The full license text is available at <http://gnu.org/licenses/gpl.html>.
++.PP
++.SH ACKNOWLEDGMENTS
++William Fletcher and Ziheng Yang (2009). INDELible: A Flexible Simulator of Biological Sequence Evolution, \fIMolecular Biology and Evolution,\fR 26(8):1879-1888.
++.SS
diff --git a/debian/patches/series b/debian/patches/series
index 8f4bdd3..367cf89 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@
 0003-added-documentation-index-page.patch
 0004-Install-HTML-docs.patch
 0005-Ensure-docs-are-distributed.patch
+0006-added-manpage.patch

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