[med-svn] [clonalframeml] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Thu Sep 21 08:44:36 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository clonalframeml.
commit c86a8ad29b330e3c6bd77ba99b04b921476cf234
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 21 10:44:17 2017 +0200
Initial Debian packaging
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 33 ++++++++++++++++++++++++
debian/copyright | 48 +++++++++++++++++++++++++++++++++++
debian/install | 1 +
debian/patches/fix_clean_target.patch | 12 +++++++++
debian/patches/series | 1 +
debian/rules | 17 +++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++
debian/watch | 3 +++
11 files changed, 134 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..334041b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+clonalframeml (1.11-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 21 Sep 2017 10:30:54 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..37d4d9f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: clonalframeml
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10)
+Standards-Version: 4.1.0
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/clonalframeml.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/clonalframeml.git
+Homepage: https://github.com/xavierdidelot/ClonalFrameML
+
+Package: clonalframeml
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Efficient Inference of Recombination in Whole Bacterial Genomes
+ ClonalFrameML is a software package that performs efficient inference of
+ recombination in bacterial genomes. ClonalFrameML was created by Xavier
+ Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of
+ aligned sequence data, but is especially aimed at analysis of whole
+ genome sequences. It is able to compare hundreds of whole genomes in a
+ matter of hours on a standard Desktop computer. There are three main
+ outputs from a run of ClonalFrameML: a phylogeny with branch lengths
+ corrected to account for recombination, an estimation of the key
+ parameters of the recombination process, and a genomic map of where
+ recombination took place for each branch of the phylogeny.
+ .
+ ClonalFrameML is a maximum likelihood implementation of the Bayesian
+ software ClonalFrame which was previously described by Didelot and
+ Falush (2007). The recombination model underpinning ClonalFrameML is
+ exactly the same as for ClonalFrame, but this new implementation is a
+ lot faster, is able to deal with much larger genomic dataset, and does
+ not suffer from MCMC convergence issues
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ebdcf8b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,48 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ClonalFrameML
+Upstream-Contact: Xavier Didelot <xavier.didelot at gmail.com>
+Source: https://github.com/xavierdidelot/ClonalFrameML/releases
+
+Files: *
+Copyright: 2013-2017
+License: GPL-3+
+
+Files: src/*.cpp
+ src/*.h
+ src/myutils/*
+ src/coalesce/*
+ src/bank/*
+Copyright: 2012-2017 Daniel Wilson and Xavier Didelot.
+License: LGPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+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.
+ .
+ On Debian systems you can find a copy of the full text of the GNU General
+ Public License at /usr/share/common-licenses/GPL-3.
+
+License: LGPL-3+
+ ClonalFrameML is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ ClonalFrameML 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 Lesser General Public License for more details.
+ .
+ On Debian systems you can find a copy of the full text of the GNU General
+ Public License at /usr/share/common-licenses/LGPL-3.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..3e2d620
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+src/ClonalFrameML usr/bin
diff --git a/debian/patches/fix_clean_target.patch b/debian/patches/fix_clean_target.patch
new file mode 100644
index 0000000..1764588
--- /dev/null
+++ b/debian/patches/fix_clean_target.patch
@@ -0,0 +1,12 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 21 Sep 2017 10:30:54 +0200
+Description: Do not fail when cleaning clean source tree
+
+--- a/src/makefile
++++ b/src/makefile
+@@ -19,4 +19,4 @@ version:
+ /bin/echo "#define ClonalFrameML_GITRevision \"`git describe --tags`\"" > version.h
+
+ clean:
+- rm $(OBJECTS)
++ rm -f $(OBJECTS)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..3dd6a58
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_clean_target.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..27a2bb7
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --sourcedirectory=src
+
+override_dh_auto_build:
+ # upstream is querying Git for a revision which is not possible here
+ # that's why we are using the Debian revision
+ echo '#define ClonalFrameML_GITRevision "v$(DEB_VERSION)"' > src/version.h
+ dh_auto_build
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..4d57a6f
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Xavier Didelot and Daniel J. Wilson
+ Title: "ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes"
+ Journal: PLoS Comput Biology
+ Year: 2015
+ Volume: 11
+ Number: 2
+ Pages: e1004041
+ DOI: 10.1371/journal.pcbi.1004041
+ PMID: 25675341
+ URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004041
+ eprint: http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004041&type=printable
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a923651
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/xavierdidelot/ClonalFrameML/releases .*/archive/v at ANY_VERSION@@ARCHIVE_EXT@
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