[med-svn] r19608 - in trunk/packages: . tantan tantan/trunk tantan/trunk/debian tantan/trunk/debian/source tantan/trunk/debian/upstream
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Mon Jul 13 21:34:05 UTC 2015
Author: sascha-guest
Date: 2015-07-13 21:34:04 +0000 (Mon, 13 Jul 2015)
New Revision: 19608
Added:
trunk/packages/tantan/
trunk/packages/tantan/trunk/
trunk/packages/tantan/trunk/debian/
trunk/packages/tantan/trunk/debian/changelog
trunk/packages/tantan/trunk/debian/compat
trunk/packages/tantan/trunk/debian/control
trunk/packages/tantan/trunk/debian/copyright
trunk/packages/tantan/trunk/debian/createmanpages
trunk/packages/tantan/trunk/debian/manpages
trunk/packages/tantan/trunk/debian/rules
trunk/packages/tantan/trunk/debian/source/
trunk/packages/tantan/trunk/debian/source/format
trunk/packages/tantan/trunk/debian/tantan.1
trunk/packages/tantan/trunk/debian/upstream/
trunk/packages/tantan/trunk/debian/upstream/metadata
trunk/packages/tantan/trunk/debian/watch
Log:
first version of tantan
Property changes on: trunk/packages/tantan/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/tantan/trunk/debian/changelog
===================================================================
--- trunk/packages/tantan/trunk/debian/changelog (rev 0)
+++ trunk/packages/tantan/trunk/debian/changelog 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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
Added: trunk/packages/tantan/trunk/debian/compat
===================================================================
--- trunk/packages/tantan/trunk/debian/compat (rev 0)
+++ trunk/packages/tantan/trunk/debian/compat 2015-07-13 21:34:04 UTC (rev 19608)
@@ -0,0 +1 @@
+9
Added: trunk/packages/tantan/trunk/debian/control
===================================================================
--- trunk/packages/tantan/trunk/debian/control (rev 0)
+++ trunk/packages/tantan/trunk/debian/control 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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
Added: trunk/packages/tantan/trunk/debian/copyright
===================================================================
--- trunk/packages/tantan/trunk/debian/copyright (rev 0)
+++ trunk/packages/tantan/trunk/debian/copyright 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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
Added: trunk/packages/tantan/trunk/debian/createmanpages
===================================================================
--- trunk/packages/tantan/trunk/debian/createmanpages (rev 0)
+++ trunk/packages/tantan/trunk/debian/createmanpages 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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 > $MANDIR/tantan.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
Property changes on: trunk/packages/tantan/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/tantan/trunk/debian/manpages
===================================================================
--- trunk/packages/tantan/trunk/debian/manpages (rev 0)
+++ trunk/packages/tantan/trunk/debian/manpages 2015-07-13 21:34:04 UTC (rev 19608)
@@ -0,0 +1 @@
+debian/tantan.1
Added: trunk/packages/tantan/trunk/debian/rules
===================================================================
--- trunk/packages/tantan/trunk/debian/rules (rev 0)
+++ trunk/packages/tantan/trunk/debian/rules 2015-07-13 21:34:04 UTC (rev 19608)
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+export DESTDIR=$(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
Property changes on: trunk/packages/tantan/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/tantan/trunk/debian/source/format
===================================================================
--- trunk/packages/tantan/trunk/debian/source/format (rev 0)
+++ trunk/packages/tantan/trunk/debian/source/format 2015-07-13 21:34:04 UTC (rev 19608)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/tantan/trunk/debian/tantan.1
===================================================================
--- trunk/packages/tantan/trunk/debian/tantan.1 (rev 0)
+++ trunk/packages/tantan/trunk/debian/tantan.1 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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/
Added: trunk/packages/tantan/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/tantan/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/tantan/trunk/debian/upstream/metadata 2015-07-13 21:34:04 UTC (rev 19608)
@@ -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
Added: trunk/packages/tantan/trunk/debian/watch
===================================================================
--- trunk/packages/tantan/trunk/debian/watch (rev 0)
+++ trunk/packages/tantan/trunk/debian/watch 2015-07-13 21:34:04 UTC (rev 19608)
@@ -0,0 +1,2 @@
+version=3
+http://cbrc3.cbrc.jp/~martin/tantan/tantan-([0-9]*).zip
More information about the debian-med-commit
mailing list