[med-svn] r4946 - in trunk/packages: . denoiser denoiser/trunk denoiser/trunk/debian denoiser/trunk/debian/patches

Sat Jun 26 19:14:19 UTC 2010

Author: moeller
Date: 2010-06-26 19:14:12 +0000 (Sat, 26 Jun 2010)
New Revision: 4946

Added:
   trunk/packages/denoiser/
   trunk/packages/denoiser/trunk/
   trunk/packages/denoiser/trunk/debian/
   trunk/packages/denoiser/trunk/debian/README.Debian
   trunk/packages/denoiser/trunk/debian/README.source
   trunk/packages/denoiser/trunk/debian/changelog
   trunk/packages/denoiser/trunk/debian/control
   trunk/packages/denoiser/trunk/debian/copyright
   trunk/packages/denoiser/trunk/debian/docs
   trunk/packages/denoiser/trunk/debian/patches/
   trunk/packages/denoiser/trunk/debian/patches/makefile
   trunk/packages/denoiser/trunk/debian/patches/series
   trunk/packages/denoiser/trunk/debian/rules
   trunk/packages/denoiser/trunk/debian/watch
Log:
A rudimentary start to package donoiser.



Property changes on: trunk/packages/denoiser/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/denoiser/trunk/debian/README.Debian
===================================================================

--- trunk/packages/denoiser/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/README.Debian	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,3 @@
+The packaging is not yet complete.
+
+Steffen

Added: trunk/packages/denoiser/trunk/debian/README.source
===================================================================
--- trunk/packages/denoiser/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/README.source	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,5 @@
+denoiser for Debian
+-------------------
+
+A central Makefile was added.
+

Added: trunk/packages/denoiser/trunk/debian/changelog
===================================================================
--- trunk/packages/denoiser/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/changelog	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,6 @@
+denoiser (0.8.5-1) unstable; urgency=low
+
+  * Initial release (Closes: #)
+
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Sat, 26 Jun 2010 20:36:02 +0200
+

Added: trunk/packages/denoiser/trunk/debian/control
===================================================================
--- trunk/packages/denoiser/trunk/debian/control	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/control	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,20 @@
+Source: denoiser
+Section: science
+Priority: extra
+Maintainer: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+Build-Depends: debhelper (>= 7), cdbs, python, ghc6
+Standards-Version: 3.8.4
+Homepage: http://www.microbio.me/denoiser/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/denoiser/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/denoiser/trunk/
+
+Package: denoiser
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
+Description: Rapid denoising of pyrosequencing amplicon data 
+ To denoise pyrosequencing amplicon data, the package exploits the
+ rank-abundance distribution.  PyroNoise uses an expectation maximization
+ (EM) algorithm to figure out the most likely sequence for every read. We,
+ instead, use a greedy scheme that can be seen as an approximation to
+ PyroNoise. According to several test data sets, the approximation gives
+ very similar results in a fraction of the time.

Added: trunk/packages/denoiser/trunk/debian/copyright
===================================================================
--- trunk/packages/denoiser/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/copyright	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,24 @@
+This work was packaged for Debian by:
+
+    Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+    and Steffen Moeller <moeller at debian.org>
+    on Sat, 26 Jun 2010 21:13:42 +0200
+
+It was downloaded from <http://www.microbio.me/denoiser/>
+
+Upstream Authors:
+
+
+Copyright:
+
+
+License:
+
+
+The Debian packaging is:
+
+    Copyright (C) 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+    and Steffen Moeller <moeller at debian.org>
+
+and is licensed under the same copyright,
+see `/usr/share/common-licenses/GPL-2'.

Added: trunk/packages/denoiser/trunk/debian/docs
===================================================================
--- trunk/packages/denoiser/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/docs	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1 @@
+FAQ.txt

Added: trunk/packages/denoiser/trunk/debian/patches/makefile
===================================================================
--- trunk/packages/denoiser/trunk/debian/patches/makefile	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/patches/makefile	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,17 @@
+Index: denoiser-0.85/Makefile
+===================================================================
+--- /dev/null	1970-01-01 00:00:00.000000000 +0000
++++ denoiser-0.85/Makefile	2010-06-26 20:58:34.000000000 +0200
+@@ -0,0 +1,12 @@
++#!/usr/bin/make -f
++
++all:
++	$(MAKE) -C FlowgramAlignment
++
++
++clean:
++	$(MAKE) -C FlowgramAlignment $@
++
++distclean: clean
++	find FlowgramAlignment -name "FlowgramAli_4frame_linux_*" | xargs -r rm
++

Added: trunk/packages/denoiser/trunk/debian/patches/series
===================================================================
--- trunk/packages/denoiser/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/patches/series	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1 @@
+makefile

Added: trunk/packages/denoiser/trunk/debian/rules
===================================================================
--- trunk/packages/denoiser/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/rules	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@


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

Added: trunk/packages/denoiser/trunk/debian/watch
===================================================================
--- trunk/packages/denoiser/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/denoiser/trunk/debian/watch	2010-06-26 19:14:12 UTC (rev 4946)
@@ -0,0 +1,2 @@
+version=3
+http://www.microbio.me/denoiser/Denoiser_([.0-9]+)\.tgz


