[med-svn] [diamond] 02/03: Initial packaging
Andreas Tille
tille at debian.org
Thu Jan 5 10:24:14 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository diamond.
commit 2fccb05a3d8adf81a6446ac15c3169240caf1337
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 5 10:58:33 2017 +0100
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 23 +++++++++++++++++++++++
debian/copyright | 22 ++++++++++++++++++++++
debian/doc-base | 13 +++++++++++++
debian/docs | 2 ++
debian/rules | 18 ++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 3 +++
10 files changed, 99 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ee75465
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+diamond (0.8.31-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Jan 2017 10:33:38 +0100
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..26f0e96
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,23 @@
+Source: diamond
+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),
+ cmake,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/diamond.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/diamond.git
+Homepage: https://github.com/bbuchfink/diamond
+
+Package: diamond
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: accelerated BLAST compatible local sequence aligner
+ DIAMOND is a sequence aligner for protein and translated DNA searches
+ and functions as a drop-in replacement for the NCBI BLAST software
+ tools. It is suitable for protein-protein search as well as DNA-protein
+ search on short reads and longer sequences including contigs and
+ assemblies, providing a speedup of BLAST ranging up to x20,000.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5e7688f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,22 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Benjamin Buchfink <buchfink at gmail.com>
+Source: https://github.com/bbuchfink/diamond
+
+Files: *
+Copyright: 2014-2016, University of Tuebingen, Benjamin Buchfink
+License: BSD-3-clause
+
+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 PART
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..573120e
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,13 @@
+Document: diamond
+Title: Benjamin Buchfink <buchfink at gmail.com>
+Author: Benjamin Buchfink <buchfink at gmail.com>
+Abstract: accelerated BLAST compatible local sequence aligner
+ DIAMOND is a sequence aligner for protein and translated DNA searches
+ and functions as a drop-in replacement for the NCBI BLAST software
+ tools. It is suitable for protein-protein search as well as DNA-protein
+ search on short reads and longer sequences including contigs and
+ assemblies, providing a speedup of BLAST ranging up to x20,000.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/diamond/diamond_manual.pdf
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..71ea9a8
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README*
+diamond_manual.pdf
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..622ff4a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,18 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# for hardening you might like to uncomment this:
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+MSSSSE3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then echo "-mssse3" ; fi)
+
+%:
+ dh $@
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
+
+build_simple:
+ MSSSSE3=$(MSSSSE3) build_simple.sh
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..6dacb3b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Benjamin Buchfink and Chao Xie and Daniel H Huson
+ Title: Fast and sensitive protein alignment using DIAMOND
+ Journal: Nature methods
+ Year: 2015
+ Volume: 12
+ Number: 1
+ Pages: 59-60
+ DOI: 10.1038/nmeth.3176
+ PMID: 25402007
+ URL: http://www.nature.com/nmeth/journal/v12/n1/abs/nmeth.3176.html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..6424c64
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/bbuchfink/diamond/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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