[med-svn] [phybin] 02/02: Add initial debian packaging
Andreas Tille
tille at debian.org
Tue Dec 8 12:53:27 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository phybin.
commit a8ce411847c39d7268ae5b9200bb86718d632872
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 8 13:42:20 2015 +0100
Add initial debian packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 137 +++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 37 +++++++++++++
debian/phybin.install | 1 +
debian/rules | 9 ++++
debian/source/format | 1 +
debian/upstream/metadata | 11 ++++
debian/watch | 3 ++
9 files changed, 205 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6b37633
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+phybin (0.3-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 08 Dec 2015 11:43:49 +0100
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..b7e0d36
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,137 @@
+Source: phybin
+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 (>= 9.0)
+ , haskell-devscripts (>= 0.8)
+ , cdbs
+ , ghc
+ , ghc-prof
+ , libghc-hunit-dev
+ , libghc-hunit-prof
+ , libghc-async-dev
+ , libghc-async-prof
+ , libghc-fgl-dev
+ , libghc-fgl-prof
+ , libghc-graphviz-dev (>= 2999.16)
+ , libghc-graphviz-prof (>= 2999.16)
+# not available , libghc-hierarchical-clustering-dev (>= 0.4)
+# not available , libghc-hierarchical-clustering-prof (>= 0.4)
+ , libghc-parsec3-dev (>= 3.1.0)
+ , libghc-parsec3-prof (>= 3.1.0)
+# not in Jessie , libghc-prettyclass-dev
+# not in Jessie , libghc-prettyclass-prof
+ , libghc-split-dev (>= 0.2)
+ , libghc-split-prof (>= 0.2)
+ , libghc-text-dev (>= 0.11)
+ , libghc-text-dev (<< 0.12)
+ , libghc-text-prof (>= 0.11)
+ , libghc-text-prof (<< 0.12)
+ , libghc-vector-dev (>= 0.10)
+ , libghc-vector-prof (>= 0.10)
+Build-Depends-Indep: ghc-doc
+ , libghc-hunit-doc
+ , libghc-async-doc
+ , libghc-fgl-doc
+ , libghc-graphviz-doc (>= 2999.16)
+# not available , libghc-hierarchical-clustering-doc (>= 0.4)
+ , libghc-parsec3-doc (>= 3.1.0)
+# not in Jessie , libghc-prettyclass-doc
+ , libghc-split-doc (>= 0.2)
+ , libghc-text-doc (>= 0.11)
+ , libghc-text-doc (<< 0.12)
+ , libghc-vector-doc (>= 0.10)
+Standards-Version: 3.9.6
+Vcs-Git: git://anonscm.debian.org/debian-med/phybin.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/phybin.git
+Homepage: http://hackage.haskell.org/package/phybin
+
+Package: libghc-phybin-dev
+Architecture: any
+Section: haskell
+Depends: ${shlibs:Depends}
+ , ${haskell:Depends}
+ , ${misc:Depends}
+Recommends: ${haskell:Recommends}
+Suggests: ${haskell:Suggests}
+Conflicts: ${haskell:Conflicts}
+Provides: ${haskell:Provides}
+Replaces: ${haskell:Replaces}
+Description: clustering phylogenetic trees in Newick format based on Robinson-Foulds distance (library)
+ This package provides a libary and executable for dealing with Newick tree files.
+ .
+ It can do simple binning of identical trees or more complex clustering based on
+ an all-to-all Robinson-Foulds distance matrix.
+ .
+ phybin produces output files that characterize the size and contents of each bin or cluster (including
+ generating GraphViz-based visual representations of the tree topologies).
+ .
+ This package provides a library for the Haskell programming language.
+ See http:///www.haskell.org/ for more information on Haskell.
+
+Package: libghc-phybin-prof
+Architecture: any
+Section: haskell
+Depends: ${shlibs:Depends}
+ , ${haskell:Depends}
+ , ${misc:Depends}
+Recommends: ${haskell:Recommends}
+Suggests: ${haskell:Suggests}
+Conflicts: ${haskell:Conflicts}
+Provides: ${haskell:Provides}
+Replaces: ${haskell:Replaces}
+Description: clustering phylogenetic trees in Newick format based on Robinson-Foulds distance (profiling)
+ This package provides a libary and executable for dealing with Newick tree files.
+ .
+ It can do simple binning of identical trees or more complex clustering based on
+ an all-to-all Robinson-Foulds distance matrix.
+ .
+ phybin produces output files that characterize the size and contents of each bin or cluster (including
+ generating GraphViz-based visual representations of the tree topologies).
+ .
+ This package provides a library for the Haskell programming language, compiled
+ for profiling. See http:///www.haskell.org/ for more information on Haskell.
+
+Package: libghc-phybin-doc
+Architecture: all
+Section: doc
+Depends: ${shlibs:Depends}
+ , ${haskell:Depends}
+ , ${misc:Depends}
+Recommends: ${haskell:Recommends}
+Suggests: ${haskell:Suggests}
+Conflicts: ${haskell:Conflicts}
+Provides: ${haskell:Provides}
+Replaces: ${haskell:Replaces}
+Description: clustering phylogenetic trees in Newick format based on Robinson-Foulds distance (doc)
+ This package provides a libary and executable for dealing with Newick tree files.
+ .
+ It can do simple binning of identical trees or more complex clustering based on
+ an all-to-all Robinson-Foulds distance matrix.
+ .
+ phybin produces output files that characterize the size and contents of each bin or cluster (including
+ generating GraphViz-based visual representations of the tree topologies).
+ .
+ This package provides the documentation for a library for the Haskell
+ programming language.
+ See http:///www.haskell.org/ for more information on Haskell.
+
+Package: phybin
+Architecture: any
+Depends: ${shlibs:Depends}
+ , ${haskell:Depends}
+ , ${misc:Depends}
+Recommends: ${haskell:Recommends}
+Suggests: ${haskell:Suggests}
+Conflicts: ${haskell:Conflicts}
+Provides: ${haskell:Provides}
+Replaces: ${haskell:Replaces}
+Description: clustering phylogenetic trees in Newick format based on Robinson-Foulds distance
+ This package provides a libary and executable for dealing with Newick tree files.
+ .
+ It can do simple binning of identical trees or more complex clustering based on
+ an all-to-all Robinson-Foulds distance matrix.
+ .
+ phybin produces output files that characterize the size and contents of each bin or cluster (including
+ generating GraphViz-based visual representations of the tree topologies).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5127d60
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,37 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: phybin
+Upstream-Contact: Ryan Newton <rrnewton at gmail.com>
+Source: https://github.com/rrnewton/PhyBin
+
+Files: *
+Copyright: 2010-2015 Ryan Newton <rrnewton at gmail.com>
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ * Neither the name of the <organization> nor the
+ names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
diff --git a/debian/phybin.install b/debian/phybin.install
new file mode 100644
index 0000000..2caba3c
--- /dev/null
+++ b/debian/phybin.install
@@ -0,0 +1 @@
+dist-ghc/build/phybin/phybin usr/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..a97581c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+DEB_CABAL_PACKAGE = phybin
+DEB_DEFAULT_COMPILER = ghc
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/hlibrary.mk
+
+build/phybin:: build-ghc-stamp
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..8ecc8df
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Ryan R. Newton and Irene L.G. Newton
+ Title: "PhyBin: binning trees by topology"
+ Journal: PeerJ
+ Year: 2013
+ Volume: 1
+ Pages: e187
+ DOI: 10.7717/peerj.187
+ PMID: 24167782
+ URL: https://peerj.com/articles/187/
+ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807594/pdf/peerj-01-187.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..4022f49
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/rrnewton/PhyBin/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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