[med-svn] [harvest-tools] 02/02: Add initial Debian packaging

Andreas Tille tille at debian.org
Tue Mar 15 13:31:09 UTC 2016 

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tille pushed a commit to branch master
in repository harvest-tools.

commit e9939c3700f9c71d3eae1e38827b6bbc6a42fc31
Author: Andreas Tille <tille at debian.org>
Date:   Tue Mar 15 14:25:39 2016 +0100

    Add initial Debian packaging
---
 debian/changelog                         |  5 ++++
 debian/clean                             |  3 +++
 debian/compat                            |  1 +
 debian/control                           | 31 +++++++++++++++++++++
 debian/copyright                         | 46 ++++++++++++++++++++++++++++++++
 debian/install                           |  1 +
 debian/patches/dynamic_linking.patch     | 15 +++++++++++
 debian/patches/fix_readme_in_setup.patch | 15 +++++++++++
 debian/patches/series                    |  2 ++
 debian/rules                             | 14 ++++++++++
 debian/source/format                     |  1 +
 debian/upstream/metadata                 | 12 +++++++++
 debian/watch                             |  3 +++
 13 files changed, 149 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..86550fe
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+harvest-tools (1.2-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 15 Mar 2016 11:08:15 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..16b8c45
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,3 @@
+Makefile
+config.log
+config.status
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..833ae69
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: harvest-tools
+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),
+               dh-autoreconf,
+               cython,
+               python-setuptools,
+               protobuf-compiler,
+               capnproto,
+               libprotobuf-dev,
+               libcapnp-dev,
+               zlib1g-dev
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/harvest-tools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/harvest-tools.git
+Homepage: http://harvest.readthedocs.org/en/latest/content/harvest-tools.html
+X-Python-Version: >= 2.7
+
+Package: harvest-tools
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: archiving and postprocessing for reference-compressed genomic multi-alignments
+ HarvestTools is a utility for creating and interfacing with Gingr files,
+ which are efficient archives that the Harvest Suite uses to store reference-
+ compressed multi-alignments, phylogenetic trees, filtered variants and
+ annotations. Though designed for use with Parsnp and Gingr, HarvestTools
+ can also be used for generic conversion between standard bioinformatics
+ file formats.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f618365
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,46 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: HarvestTools
+Source: https://github.com/marbl/harvest-tools/releases
+
+Files: *
+Copyright: 2014 Brian Ondov, Todd Treangen, and Adam Phillippy
+                Battelle National Biodefense Institute (BNBI)
+License: BSD-3-clause
+Comment:
+ This Software was prepared for the Department of Homeland Security
+ (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
+ part of contract HSHQDC-07-C-00020 to manage and operate the National
+ Biodefense Analysis and Countermeasures Center (NBACC), a Federally
+ Funded Research and Development Center.
+
+Files: debian/*
+Copyright: 2016 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:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. 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.
+ .
+ 3. Neither the name of the copyright holder 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 THE COPYRIGHT
+ HOLDER OR CONTRIBUTORS 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/install b/debian/install
new file mode 100644
index 0000000..6f01b90
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+harvesttools	usr/bin
diff --git a/debian/patches/dynamic_linking.patch b/debian/patches/dynamic_linking.patch
new file mode 100644
index 0000000..4a8d1ec
--- /dev/null
+++ b/debian/patches/dynamic_linking.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Mar 2016 11:08:15 +0100
+Description: Use dynamic linking against libprotobuf and libcapnp
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -26,7 +26,7 @@ OBJECTS=$(SOURCES:.cpp=.o) src/harvest/p
+ all : harvesttools libharvest.a
+ 
+ harvesttools : libharvest.a src/harvest/memcpyWrap.o
+-	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o harvesttools src/harvest/memcpyWrap.o libharvest.a @protobuf@/lib/libprotobuf.a @capnp@/lib/libcapnp.a @capnp@/lib/libkj.a -lstdc++ -lz -lm -lpthread
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o harvesttools src/harvest/memcpyWrap.o libharvest.a -lprotobuf -lcapnp -lkj -lstdc++ -lz -lm -lpthread
+ 
+ libharvest.a : $(OBJECTS)
+ 	ar -cr libharvest.a $(OBJECTS)
diff --git a/debian/patches/fix_readme_in_setup.patch b/debian/patches/fix_readme_in_setup.patch
new file mode 100644
index 0000000..df790a5
--- /dev/null
+++ b/debian/patches/fix_readme_in_setup.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Mar 2016 11:08:15 +0100
+Description: There is no such file README but README.md
+
+--- a/setup.py
++++ b/setup.py
+@@ -23,7 +23,7 @@ setup(
+     license = "Perl Artistic License",
+     keywords = "multialignment snps bionformatics",
+     url = "http://github.com/MGI/ParSNP/wiki",
+-    long_description=read('README'),
++    long_description=read('README.md'),
+     classifiers=[
+         "Development Status :: 3 - Alpha"
+     ],
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7299241
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_readme_in_setup.patch
+dynamic_linking.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c2af8b3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+	dh $@ --with autoreconf
+
+override_dh_auto_configure:
+	dh_auto_configure -- --with-protobuf=/usr --with-capnp=/usr
+
+override_dh_auto_install:
+	echo "do nothing since upstream is just symlinking against build tree"
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..86f2d9d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Todd J. Treangen and Brian D. Ondov and Sergey Koren and Adam M. Phillippy
+  Title: Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes
+  Journal: bioRxiv
+  Year: 2014
+  Volume: 15
+  Number: 11
+  Pages: 524
+  DOI: 10.1101/007351 
+  PMID: 25410596
+  URL: http://biorxiv.org/content/early/2014/10/20/007351
+  eprint: http://biorxiv.org/content/early/2014/10/20/007351.full.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5ac0516
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/marbl/harvest-tools/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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