[med-svn] [mash] 02/02: add initial packaging
Sascha Steinbiss
satta at debian.org
Tue Jul 19 10:59:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository mash.
commit d48ca2ca58128200846fd2c04465a68874cab737
Author: Sascha Steinbiss <satta at debian.org>
Date: Tue Jul 19 10:58:25 2016 +0000
add initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 28 ++++++++++++++++++++++++++++
debian/copyright | 46 ++++++++++++++++++++++++++++++++++++++++++++++
debian/rules | 27 +++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 4 ++++
8 files changed, 123 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..c62920f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+mash (1.1-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #831781)
+
+ -- Sascha Steinbiss <satta at debian.org> Tue, 19 Jul 2016 10:12:44 +0000
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..ed8f550
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: mash
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <satta at debian.org>
+Build-Depends: debhelper (>= 9),
+ capnproto,
+ libcapnp-dev,
+ libgsl-dev,
+ dh-autoreconf,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: https://mash.readthedocs.io
+
+Package: mash
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: fast genome and metagenome distance estimation using MinHash
+ Mash uses MinHash locality-sensitive hashing to reduce large biosequences to
+ a representative sketch and rapidly estimate pairwise distances between
+ genomes or metagenomes. Mash sketch databases effectively delineate known
+ species boundaries, allow construction of approximate phylogenies, and can be
+ searched in seconds using assembled genomes or raw sequencing runs from
+ Illumina, Pacific Biosciences, and Oxford Nanopore.
+ For metagenomics, Mash scales to thousands of samples and can replicate Human
+ Microbiome Project and Global Ocean Survey results in a fraction of the time.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..cb0fa43
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,46 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Mash
+Upstream-Contact: Adap Phillippy <adam.phillippy at nih.gov>
+Source: https://github.com/marbl/Mash
+
+Files: *
+Copyright: © 2015 Battelle National Biodefense Institute (BNBI)
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: © 2016 Sascha Steinbiss <satta at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ 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.
+ .
+ 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/rules b/debian/rules
new file mode 100755
index 0000000..0115680
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --with autoreconf --parallel
+
+override_dh_auto_configure:
+ dh_auto_configure -- --with-capnp=/usr --with-gsl=/usr --prefix=$(CURDIR)/debian/mash/usr
+
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..606fe7a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Brian D. Ondovi and Todd J. Treangen and Páll Melsted and Adam B. Mallonee and Nicholas H. Bergman and Sergey Koren and Adam M. Phillippy
+ Title: "Mash: fast genome and metagenome distance estimation using MinHash"
+ Journal: Genome Biology
+ Year: 2016
+ Volume: 17
+ Pages: 132
+ DOI: 10.1186/s13059-016-0997-x
+ PMID: 27323842
+ URL: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
+ eprint: http://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-016-0997-x?site=genomebiology.biomedcentral.com
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..97e12f1
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="compress=xz" \
+https://github.com/marbl/Mash/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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