[med-svn] r18573 - in trunk/packages/vsearch: . trunk trunk/debian trunk/debian/source

[Timothy Booth]

Author: tbooth-guest
Date: 2015-01-13 14:27:07 +0000 (Tue, 13 Jan 2015)
New Revision: 18573

Added:
   trunk/packages/vsearch/trunk/
   trunk/packages/vsearch/trunk/debian/
   trunk/packages/vsearch/trunk/debian/changelog
   trunk/packages/vsearch/trunk/debian/compat
   trunk/packages/vsearch/trunk/debian/control
   trunk/packages/vsearch/trunk/debian/copyright
   trunk/packages/vsearch/trunk/debian/docs
   trunk/packages/vsearch/trunk/debian/install
   trunk/packages/vsearch/trunk/debian/rules
   trunk/packages/vsearch/trunk/debian/source/
   trunk/packages/vsearch/trunk/debian/source/format
   trunk/packages/vsearch/trunk/debian/watch
Removed:
   trunk/packages/vsearch/debian/
Log:
And here's the actual files


Added: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/changelog	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,5 @@
+vsearch (1.0.7) trusty; urgency=low
+
+  * Initial package
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 09 Jan 2015 17:13:35 +0000

Added: trunk/packages/vsearch/trunk/debian/compat
===================================================================
--- trunk/packages/vsearch/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/compat	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1 @@
+9

Added: trunk/packages/vsearch/trunk/debian/control
===================================================================
--- trunk/packages/vsearch/trunk/debian/control	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/control	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,27 @@
+Source: vsearch
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9), zlib1g-dev, libbz2-dev, python-markdown
+Standards-Version: 3.9.6
+Homepage: https://github.com/torognes/vsearch/
+
+Package: vsearch
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: tool for processing metagenomic sequences
+ Open and free 64-bit multithreaded tool for processing metagenomic sequences,
+ including searching, clustering, chimera detection, dereplication, sorting,
+ masking and shuffling
+ .
+ The aim of this project is to create an alternative to the USEARCH tool
+ developed by Robert C. Edgar (2010). The new tool should:
+ .
+  - have open source code with an appropriate open source license
+  - be free of charge, gratis
+  - have a 64-bit design that handles very large databases and much more
+    than 4GB of memory
+  - be as accurate or more accurate than usearch
+  - be as fast or faster than usearch

Added: trunk/packages/vsearch/trunk/debian/copyright
===================================================================
--- trunk/packages/vsearch/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/copyright	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,12 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: VSEARCH
+Upstream-Contact: Torbjørn Rognes
+Source: https://github.com/torognes/vsearch/
+
+Files: *
+Copyright: © 2014-2015 Torbjorn Rognes & Tomas Flouri
+License: Affero-GPL-3
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: GPL-3

Added: trunk/packages/vsearch/trunk/debian/docs
===================================================================
--- trunk/packages/vsearch/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/docs	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1 @@
+*.html

Added: trunk/packages/vsearch/trunk/debian/install
===================================================================
--- trunk/packages/vsearch/trunk/debian/install	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/install	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,3 @@
+src/vsearch	/usr/bin
+src/vsearch-gz	/usr/bin
+src/vsearch-bz	/usr/bin

Added: trunk/packages/vsearch/trunk/debian/rules
===================================================================
--- trunk/packages/vsearch/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/rules	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,36 @@
+#!/usr/bin/make -f
+# debian/rules for bowtie
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+%:
+	dh $@ --sourcedirectory=src
+
+override_dh_auto_build:
+	# See notes in README.source
+	dh_auto_build -- -f Makefile.BZLIB
+	dh_auto_clean
+	dh_auto_build -- -f Makefile.ZLIB
+	dh_auto_clean
+	dh_auto_build
+	markdown_py -f README.html README.md
+
+override_dh_auto_test:
+	cd data && tar -xvzf simm.tar.gz
+	cd test && \
+	for t in *.sh ; do \
+	    bash $$t v ; \
+	done
+
+override_dh_clean:
+	dh_clean
+	rm -rf data/simm
+	find test -mindepth 1 -not -name '*.sh' -delete
+	rm -f README.html


Property changes on: trunk/packages/vsearch/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/vsearch/trunk/debian/source/format
===================================================================
--- trunk/packages/vsearch/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/source/format	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/vsearch/trunk/debian/watch
===================================================================
--- trunk/packages/vsearch/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/watch	2015-01-13 14:27:07 UTC (rev 18573)
@@ -0,0 +1,4 @@
+version=3
+
+opts="downloadurlmangle=s/\/tree\/(.*)/\/archive\/$1.tar.gz/" \
+  https://github.com/torognes/vsearch/ .*/tree/v([0-9.rc-]+)