[med-svn] [Git][med-team/bio-rainbow][master] 11 commits: * Enhance description
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 4 14:08:59 BST 2018
Andreas Tille pushed to branch master at Debian Med / bio-rainbow
Commits:
a22b2ef8 by Andreas Tille at 2018-07-04T14:41:33+02:00
* Enhance description
* cme fix dpkg-control
* Standards-Version: 4.1.4
* Point VCS fields to Salsa
- - - - -
b5d038fb by Andreas Tille at 2018-07-04T14:49:00+02:00
Upstream source was repackaged to remove some files - do this with Files-Excluded instead of get-orig-source and express it with +dfsg prefix
- - - - -
210b7c06 by Andreas Tille at 2018-07-04T14:49:17+02:00
New upstream version 2.0.4+dfsg
- - - - -
f6ae0771 by Andreas Tille at 2018-07-04T14:49:18+02:00
Update upstream source from tag 'upstream/2.0.4+dfsg'
Update to upstream version '2.0.4+dfsg'
with Debian dir 5d5eb3b6290ce4f18a004a660ac402866fadcde3
- - - - -
a8b362bb by Andreas Tille at 2018-07-04T14:49:59+02:00
debhelper 11
- - - - -
cb63fcfb by Andreas Tille at 2018-07-04T14:54:50+02:00
Lintian override for script-with-language-extension
- - - - -
39991690 by Andreas Tille at 2018-07-04T14:56:49+02:00
DEP3
- - - - -
19479ac3 by Andreas Tille at 2018-07-04T14:58:14+02:00
DEP5
- - - - -
a67cd2bd by Andreas Tille at 2018-07-04T15:06:54+02:00
hardening+=all
- - - - -
f3d0b74b by Andreas Tille at 2018-07-04T15:07:46+02:00
Really fix copyright
- - - - -
eda88020 by Andreas Tille at 2018-07-04T15:08:15+02:00
Fix description
- - - - -
11 changed files:
- − ._Makefile
- − ._tags
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- − debian/get-orig-source
- + debian/lintian-overrides
- debian/patches/rename_binary.patch
- debian/rules
- debian/watch
Changes:
=====================================
._Makefile deleted
=====================================
Binary files a/._Makefile and /dev/null differ
=====================================
._tags deleted
=====================================
Binary files a/._tags and /dev/null differ
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,24 @@
-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 at 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 at debian.org> Wed, 04 Jul 2018 14:39:26 +0200
bio-rainbow (2.0.4-1) unstable; urgency=low
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,16 +1,34 @@
Source: bio-rainbow
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou at 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
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,6 +1,15 @@
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 at genomics.org.cn>
+ 2003-2006, Heng Li <liheng at genomics.org.cn>
+ 2011, Jue Ruan <ruanjue at gmail.com>
+License: GPL-3+
Files: stdaln.*
Copyright: 2003-2006, Li Heng <liheng at genomics.org.cn>
@@ -18,32 +27,11 @@ 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 at genomics.org.cn>
- 2003-2006, Heng Li <liheng at genomics.org.cn>
- 2011, Jue Ruan <ruanjue at 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 at 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
the Free Software Foundation; either version 2 of the License, or
@@ -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 deleted
=====================================
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/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
=====================================
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1,2 @@
+# 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
=====================================
--- a/debian/patches/rename_binary.patch
+++ b/debian/patches/rename_binary.patch
@@ -1,3 +1,7 @@
+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
=====================================
--- a/debian/rules
+++ b/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
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,4 @@
-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)))
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1
--
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1
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