debian/changelog

-bio-rainbow (2.0.4-2) UNRELEASED; urgency=low
+bio-rainbow (2.0.4+dfsg-1) UNRELEASED; urgency=medium
 
+  * Team upload.
+
+  [ Steffen Moeller ]
   * Created debian/upstream/metadata
-  * debian/control: updated standards-version to 4.1.0
 
- -- Steffen Moeller <moeller@debian.org>  Fri, 17 Nov 2017 23:51:08 +0100
+  [ Andreas Tille ]
+  * Enhance description
+  * cme fix dpkg-control
+  * Standards-Version: 4.1.4
+  * Point VCS fields to Salsa
+  * Upstream source was repackaged to remove some files - do this with
+    Files-Excluded instead of get-orig-source and express it with +dfsg prefix
+  * debhelper 11
+  * Lintian override for script-with-language-extension
+  * DEP3
+  * DEP5
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Jul 2018 14:39:26 +0200
 
 bio-rainbow (2.0.4-1) unstable; urgency=low
 

debian/compat

-9
+11

debian/control

 Source: bio-rainbow
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Olivier Sallou <osallou@debian.org>
-Build-Depends: debhelper (>= 9), help2man
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-rainbow.git
-Vcs-Git: git://anonscm.debian.org/debian-med/bio-rainbow.git
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+               help2man
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow
+Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git
 Homepage: http://sourceforge.net/projects/bio-rainbow/
 
 Package: bio-rainbow
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${perl:Depends}
 Description: clustering and assembling short reads for bioinformatics
- Efficient tool for clustering and assembling short reads, especially for RAD.
+ Efficient tool for clustering and assembling short reads,
+ especially for RAD.
+ .
+ Rainbow is developed to provide an ultra-fast and memory-efficient
+ solution to clustering and assembling short reads produced by RAD-seq.
+ First, Rainbow clusters reads using a spaced seed method. Then, Rainbow
+ implements a heterozygote calling like strategy to divide potential
+ groups into haplotypes in a top-down manner. long a guided tree, it
+ iteratively merges sibling leaves in a bottom-up manner if they are
+ similar enough. Here, the similarity is defined by comparing the 2nd
+ reads of a RAD segment. This approach tries to collapse heterozygote
+ while discriminate repetitive sequences. At last, Rainbow uses a greedy
+ algorithm to locally assemble merged reads into contigs. Rainbow not
+ only outputs the optimal but also suboptimal assembly results. Based on
+ simulation and a real guppy RAD-seq data, it is shown that Rainbow is
+ more competent than the other tools in dealing with RAD-seq data.

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: bio-rainbow
+Upstream-Name: Rainbow
 Source: http://sourceforge.net/projects/bio-rainbow/
+Files-Excluded: */.*.*
+                */._*
+                */*.bak
+
+Files: *
+Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn>
+           2003-2006, Heng Li <liheng@genomics.org.cn>
+           2011, Jue Ruan <ruanjue@gmail.com>
+License: GPL-3+
 
 Files: stdaln.*
 Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn>
@@ -18,31 +27,10 @@ License: LGPL-2.1+
  On Debian systems, the complete text of the GNU Lesser General
  Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".
 
-
-Files: *
-Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn>
-           2003-2006, Heng Li <liheng@genomics.org.cn>
-           2011, Jue Ruan <ruanjue@gmail.com>
-License: GPL-3+
- This package 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 package 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 <https://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-
-
 Files: debian/*
 Copyright: 2015 Olivier Sallou <osallou@debian.org>
+License: GPL-3+
+
 License: GPL-3+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
@@ -54,8 +42,5 @@ License: GPL-3+
  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 <https://www.gnu.org/licenses/>
- .
  On Debian systems, the complete text of the GNU General
  Public License version 3 can be found in "/usr/share/common-licenses/GPL-2".

debian/get-orig-source

-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download --no-symlink |
-    grep "Newest version on remote site is .* local version is .*" |
-    head -n 1 |
-    sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
-mkdir -p ../tarballs
-
-cd ../tarballs
-
-UTAR="rainbow_${VERSION}.tar.gz"
-
-mv ../${UTAR} .
-tar -xzf ${UTAR}
-
-mv rainbow_${VERSION} $PKG-${VERSION}.orig
-cd $PKG-${VERSION}.orig
-  rm .*.c
-  rm .*.h
-  rm .*.pl
-  rm .*.bak
-  rm .*.txt
-cd ..
-
-BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
-rm -rf ${PKG}-${VERSION}.orig
-
-rm ${UTAR}

debian/lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+bio-rainbow: script-with-language-extension usr/bin/*.pl

debian/patches/rename_binary.patch

+Author: Olivier Sallou
+Last-Update: 2015-08-17 13:26:07 +0000
+Description: Avoid file name conflict with rainbow package and rename to bio-rainbow
+
 --- a/Makefile
 +++ b/Makefile
 @@ -16,9 +16,9 @@

debian/rules

@@ -7,8 +7,7 @@
 DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/default.mk
 
-# see FEATURE AREAS in dpkg-buildflags(1)
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 # see ENVIRONMENT in dpkg-buildflags(1)
 # package maintainers to append CFLAGS
@@ -25,5 +24,3 @@ override_dh_installman:
 	help2man --no-discard-stderr  ./bio-rainbow > bio-rainbow.1
 	dh_installman
 
-get-orig-source:
-	debian/get-orig-source

debian/watch

-version=3
+version=4
 
-http://sf.net/bio-rainbow/rainbow_(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+   http://sf.net/bio-rainbow/rainbow_(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))