This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository tantan.
commit 4b5cee3d77424e9feba9e75f4c1e62a392d932db Author: Sascha Steinbiss <[email protected]> Date: Thu Feb 11 09:45:52 2016 +0000 re-add debian dir --- debian/changelog | 7 ++++++ debian/compat | 1 + debian/control | 20 +++++++++++++++++ debian/copyright | 31 ++++++++++++++++++++++++++ debian/createmanpages | 16 +++++++++++++ debian/lintian-overrides | 1 + debian/manpages | 1 + debian/rules | 16 +++++++++++++ debian/source/format | 1 + debian/tantan.1 | 58 ++++++++++++++++++++++++++++++++++++++++++++++++ debian/upstream/edam | 13 +++++++++++ debian/upstream/metadata | 11 +++++++++ debian/watch | 2 ++ 13 files changed, 178 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..c9d12a7 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,7 @@ +tantan (13-1) unstable; urgency=low + + * Initial release (Closes: #793907) + * Add missing copyright holder in d/copyright + * Fix machine readable license code + + -- Sascha Steinbiss <[email protected]> Tue, 04 Aug 2015 23:24:50 +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 <[email protected]> +Uploaders: Sascha Steinbiss <[email protected]> +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..d9f1bd7 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,31 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: tantan +Source: http://www.cbrc.jp/tantan/ + +Files: * +Copyright: © 2010 Martin Frith <[email protected]> + © 2008 Michiaki Hamada <[email protected]> + © Stephen Altschul <[email protected]> + © Yi-Kuo Yu <[email protected]> +License: GPL-3+ + +Files: debian/* +Copyright: © 2015 Sascha Steinbiss <[email protected]> +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. 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 > $MANDIR/tantan.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + diff --git a/debian/lintian-overrides b/debian/lintian-overrides new file mode 100644 index 0000000..8182eb8 --- /dev/null +++ b/debian/lintian-overrides @@ -0,0 +1 @@ +tantan binary: hardening-no-fortify-functions * diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..a6132f0 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/tantan.1 diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..77b507c --- /dev/null +++ b/debian/rules @@ -0,0 +1,16 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +export DESTDIR=$(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: [email protected] +.br +Home page: http://www.cbrc.jp/tantan/ diff --git a/debian/upstream/edam b/debian/upstream/edam new file mode 100644 index 0000000..b619a8f --- /dev/null +++ b/debian/upstream/edam @@ -0,0 +1,13 @@ +ontology: EDAM (1.12) +topic: + - Sequence composition, complexity and repeats +scopes: + - name: summary + function: + - Sequence masking + inputs: + - data: Sequence + formats: [FASTA] + outputs: + - data: Sequence + formats: [FASTA] 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tantan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
