[med-svn] r18585 - in trunk/packages/swarm-cluster/trunk/debian: . source
Timothy Booth
tbooth-guest at moszumanska.debian.org
Mon Jan 19 14:57:43 UTC 2015
Author: tbooth-guest
Date: 2015-01-19 14:57:43 +0000 (Mon, 19 Jan 2015)
New Revision: 18585
Added:
trunk/packages/swarm-cluster/trunk/debian/README.Debian
trunk/packages/swarm-cluster/trunk/debian/changelog
trunk/packages/swarm-cluster/trunk/debian/compat
trunk/packages/swarm-cluster/trunk/debian/control
trunk/packages/swarm-cluster/trunk/debian/copyright
trunk/packages/swarm-cluster/trunk/debian/docs
trunk/packages/swarm-cluster/trunk/debian/install
trunk/packages/swarm-cluster/trunk/debian/manpages
trunk/packages/swarm-cluster/trunk/debian/rules
trunk/packages/swarm-cluster/trunk/debian/source/
trunk/packages/swarm-cluster/trunk/debian/source/format
Log:
This builds for Bio-Linux. May need cleaning up for Lintian compliance.
Added: trunk/packages/swarm-cluster/trunk/debian/README.Debian
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/README.Debian 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,3 @@
+This swarm package will not work on all CPUs as it requires SSE3 instructions.
+
+The companion scripts mentioned in the manual are in /usr/share/swarm
Added: trunk/packages/swarm-cluster/trunk/debian/changelog
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/changelog (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/changelog 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,5 @@
+swarm (1.2.18-0biolinux1) trusty; urgency=medium
+
+ * Initial release for Bio-Linux
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 26 Sep 2014 12:11:38 +0100
Added: trunk/packages/swarm-cluster/trunk/debian/compat
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/compat (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/compat 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1 @@
+9
Added: trunk/packages/swarm-cluster/trunk/debian/control
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/control (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/control 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,28 @@
+Source: swarm
+Section: science
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 9), man-db, ghostscript
+Standards-Version: 3.9.5
+Homepage: https://github.com/torognes/swarm
+XS-Autobuild: yes
+Vcs-Git: git://git.debian.org/git/debian-med/abyss.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/abyss.git
+
+Package: swarm
+Architecture: amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: python
+Description: robust and fast clustering method for amplicon-based studies
+ The purpose of swarm is to provide a novel clustering algorithm to handle large
+ sets of amplicons. Traditional clustering algorithms results are strongly
+ input-order dependent, and rely on an arbitrary global clustering threshold.
+ swarm results are resilient to input-order changes and rely on a small local
+ linking threshold d, the maximum number of differences between two amplicons.
+ swarm forms stable high-resolution clusters, with a high yield of biological
+ information.
+ .
+ To cite swarm, please refer to:
+ Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014)
+ Swarm: robust and fast clustering method for amplicon-based studies.
+ PeerJ 2:e593 http://dx.doi.org/10.7717/peerj.593
Added: trunk/packages/swarm-cluster/trunk/debian/copyright
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/copyright (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/copyright 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: swarm
+Upstream-Contact: Torbjorn Rognes <torognes at ifi.uio.no>
+Source: https://github.com/torognes/swarm
+
+Files: *
+Copyright: (C) 2012-2014 Torbjorn Rognes and Frederic Mahe
+License: Affero GPL-3
+
+Files: cityhash/*
+Copyright: (c) 2011 Google, Inc.
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: debian/*
+Copyright: 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: GPL-3
Added: trunk/packages/swarm-cluster/trunk/debian/docs
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/docs (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/docs 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,2 @@
+*.pdf
+README.md
Added: trunk/packages/swarm-cluster/trunk/debian/install
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/install (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/install 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,2 @@
+swarm /usr/bin
+scripts /usr/share/swarm/
Added: trunk/packages/swarm-cluster/trunk/debian/manpages
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/manpages (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/manpages 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1 @@
+*.1
Added: trunk/packages/swarm-cluster/trunk/debian/rules
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/rules (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/rules 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ dh_auto_build
+ man -t ./swarm.1 | ps2pdf -sPAPERSIZE=a4 - > swarm_manual.pdf
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf Linux Mac swarm_manual.pdf*
+
Property changes on: trunk/packages/swarm-cluster/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/swarm-cluster/trunk/debian/source/format
===================================================================
--- trunk/packages/swarm-cluster/trunk/debian/source/format (rev 0)
+++ trunk/packages/swarm-cluster/trunk/debian/source/format 2015-01-19 14:57:43 UTC (rev 18585)
@@ -0,0 +1 @@
+3.0 (quilt)
More information about the debian-med-commit
mailing list