[med-svn] [tantan] 01/14: first version of tantan

Sascha Steinbiss sascha at steinbiss.name
Mon Feb 15 22:24:59 UTC 2016 

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sascha-guest pushed a commit to branch master
in repository tantan.

commit 40fcc8fa664f8c00f82827e16824173e74edeada
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Jul 13 21:34:04 2015 +0000

    first version of tantan
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 20 +++++++++++++++++
 debian/copyright         | 28 +++++++++++++++++++++++
 debian/createmanpages    | 16 +++++++++++++
 debian/manpages          |  1 +
 debian/rules             | 16 +++++++++++++
 debian/source/format     |  1 +
 debian/tantan.1          | 58 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/upstream/metadata | 11 +++++++++
 debian/watch             |  2 ++
 11 files changed, 159 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e7e89c0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+tantan (13-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #XXXXXX)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Mon, 13 Jul 2015 20:56:22 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..bf940f1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,20 @@
+Source: tantan
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: http://www.cbrc.jp/tantan/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/tantan/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/tantan/trunk/
+
+Package: tantan
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: low complexity and tandem repeat masker for biosequences
+ tantan is a tool to mask simple regions (low complexity and short-period tandem
+ repeats) in DNA, RNA, and protein sequences. The aim of tantan is to prevent
+ false predictions when searching for homologous regions between two sequences.
+ Simple repeats often align strongly to each other, causing false homology
+ predictions.
\ No newline at end of file
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6078d23
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: tantan
+Source: http://www.cbrc.jp/tantan/
+
+Files: *
+Copyright: © 2011 Martin Frith <tantan at cbrc.jp>
+License: GPL-3
+
+Files: debian/*
+Copyright: 2015 Sascha Steinbiss <sascha at steinbiss.name>
+License: GPL-3
+
+License: GPL-3
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+ .
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian Systems you can find a copy of the text of GPL version 3
+ at /usr/share/common-licenses/GPL-3.
\ No newline at end of file
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..c3f522b
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name='low complexity and tandem repeat masker for biosequences' \
+            --version-string="$VERSION" tantan > $MANDIR/tantan.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..a6132f0
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/tantan.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..77b507c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+export DESTDIR=$(CURDIR)/debian/tantan/usr
+export DH_ALWAYS_EXCLUDE=.gitignore
+
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
+%:
+	dh $@
+
+override_dh_auto_install:
+	make prefix=$(DESTDIR) install
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tantan.1 b/debian/tantan.1
new file mode 100644
index 0000000..6d8f296
--- /dev/null
+++ b/debian/tantan.1
@@ -0,0 +1,58 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH TANTAN "1" "July 2015" "tantan 13" "User Commands"
+.SH NAME
+tantan \- low complexity and tandem repeat masker for biosequences
+.SH SYNOPSIS
+.B tantan
+[\fI\,options\/\fR] \fI\,fasta-sequence-file(s)\/\fR
+.SH DESCRIPTION
+Find simple repeats in sequences
+.SS "Options (default settings):"
+.TP
+\fB\-p\fR
+interpret the sequences as proteins
+.TP
+\fB\-x\fR
+letter to use for masking, instead of lowercase
+.TP
+\fB\-c\fR
+preserve uppercase/lowercase in non\-masked regions
+.TP
+\fB\-m\fR
+file for letter pair scores (+1/\-1, but \fB\-p\fR selects BLOSUM62)
+.TP
+\fB\-r\fR
+probability of a repeat starting per position (0.005)
+.TP
+\fB\-e\fR
+probability of a repeat ending per position (0.05)
+.TP
+\fB\-w\fR
+maximum tandem repeat period to consider (100, but \fB\-p\fR selects 50)
+.TP
+\fB\-d\fR
+probability decay per period (0.9)
+.TP
+\fB\-a\fR
+gap existence cost (0)
+.TP
+\fB\-b\fR
+gap extension cost (infinite: no gaps)
+.TP
+\fB\-s\fR
+minimum repeat probability for masking (0.5)
+.TP
+\fB\-f\fR
+output type: 0=masked sequence, 1=repeat probabilities,
+.IP
+2=repeat counts, 3=BED (0)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show help message, then exit
+.TP
+\fB\-\-version\fR
+show version information, then exit
+.SH "REPORTING BUGS"
+Report bugs to: tantan at cbrc.jp
+.br
+Home page: http://www.cbrc.jp/tantan/
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..c69c035
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+  Author: Frith, Martin C.
+  Title: A new repeat-masking method enables specific detection of homologous sequences
+  Journal: Nucleic Acids Research
+  Year: 2011
+  Volume: 39
+  Number: 4
+  Pages: e23
+  DOI: 10.1093/nar/gkq1212
+  PMID: 21109538
+  URL: http://nar.oxfordjournals.org/content/39/4/e23.abstract
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5441fb1
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://cbrc3.cbrc.jp/~martin/tantan/tantan-([0-9]*).zip

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