[med-svn] r6751 - in trunk/packages/denoiser/trunk/debian: . patches

Mon May 2 17:09:27 UTC 2011

Author: moeller
Date: 2011-05-02 17:09:20 +0000 (Mon, 02 May 2011)
New Revision: 6751

Modified:
   trunk/packages/denoiser/trunk/debian/README.Debian
   trunk/packages/denoiser/trunk/debian/changelog
   trunk/packages/denoiser/trunk/debian/control
   trunk/packages/denoiser/trunk/debian/get-orig-source
   trunk/packages/denoiser/trunk/debian/patches/fix_upstream_clean_target.patch
   trunk/packages/denoiser/trunk/debian/patches/set_debian_path.patch
   trunk/packages/denoiser/trunk/debian/rules
Log:
Initial upload to experimental.


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

--- trunk/packages/denoiser/trunk/debian/README.Debian	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/README.Debian	2011-05-02 17:09:20 UTC (rev 6751)
@@ -1,3 +1,9 @@
-The packaging is not yet complete.
+The packaging is not yet complete, but looks already fairly good.
+The package was not yet tested in production environment, please
+give feedback to have it migrate to unstable.
 
+The role of python-support is not clear to me. Lintian complains
+when this dependency is not set, and indeed, it is called during
+the build.
+
 Steffen

Modified: trunk/packages/denoiser/trunk/debian/changelog
===================================================================
--- trunk/packages/denoiser/trunk/debian/changelog	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/changelog	2011-05-02 17:09:20 UTC (rev 6751)
@@ -1,5 +1,11 @@
-denoiser (0.8.5.1-1) unstable; urgency=low
+denoiser (0.9.1-1) experimental; urgency=low
 
-  * Initial release (Closes: #587274)
+  * New upstream release (Closes: #587274).
 
+ -- Steffen Moeller <moeller at debian.org>  Mon, 02 May 2011 18:03:45 +0200
+
+denoiser (0.8.5.1-1) UNRELEASED; urgency=low
+
+  * Initial release.
+
  -- Andreas Tille <tille at debian.org>  Fri, 25 Feb 2011 20:26:49 +0100

Modified: trunk/packages/denoiser/trunk/debian/control
===================================================================
--- trunk/packages/denoiser/trunk/debian/control	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/control	2011-05-02 17:09:20 UTC (rev 6751)
@@ -2,18 +2,16 @@
 Section: contrib/science
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>,
- Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), python-support, python, ghc6
-Standards-Version: 3.9.1
+Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), ghc6, python-support (>= 0.90)
+Standards-Version: 3.9.2
 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}, ${python:Depends}, python-cogent
+Depends: ${shlibs:Depends}, ${misc:Depends}, python-cogent, python, python-support (>= 0.90)
 Description: Rapid denoising of pyrosequencing amplicon data 
  To denoise pyrosequencing amplicon data, the package exploits the
  rank-abundance distribution.  PyroNoise uses an expectation maximization

Modified: trunk/packages/denoiser/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/denoiser/trunk/debian/get-orig-source	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/get-orig-source	2011-05-02 17:09:20 UTC (rev 6751)
@@ -3,6 +3,8 @@
 # explicite link to a downloadable tarball on the web page and the source is
 # only in SVN
 
+set -e
+
 UNAME=Denoiser
 UURL=http://www.microbio.me/denoiser/
 
@@ -19,13 +21,20 @@
 fi
 
 VERSION=`echo $DVERSION | sed -e 's/\.//g' -e 's/^\([0-9]\)/\1./'`
-cd ..
-mkdir -p tarballs
-cd tarballs
 
+origDir=../tarballs
+if [ -r .svn/deb-layout ]; then
+	. .svn/deb-layout
+fi
+
+mkdir -p "$origDir"
+cd "$origDir"
+
 UDIR="$UNAME"_"$VERSION"
 UTAR="$UDIR".tgz
 # wget $UURL""$UTAR"
+
+echo "Expecting file '$UTAR' in `pwd`."
 tar -xzf "$UTAR"
 
 find "$UDIR"/FlowgramAlignment -name "FlowgramAli_4frame_linux_*" | xargs -r rm

Modified: trunk/packages/denoiser/trunk/debian/patches/fix_upstream_clean_target.patch
===================================================================
--- trunk/packages/denoiser/trunk/debian/patches/fix_upstream_clean_target.patch	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/patches/fix_upstream_clean_target.patch	2011-05-02 17:09:20 UTC (rev 6751)
@@ -3,9 +3,11 @@
 Reported-Upstream: TODO
 Description: Make sure clean target will never fail
 
---- Denoiser_0.851.orig/FlowgramAlignment/Makefile
-+++ Denoiser_0.851/FlowgramAlignment/Makefile
-@@ -8,6 +8,6 @@
+Index: Denoiser_0.91/FlowgramAlignment/Makefile
+===================================================================
+--- Denoiser_0.91.orig/FlowgramAlignment/Makefile	2011-03-10 07:05:47.000000000 +0100
++++ Denoiser_0.91/FlowgramAlignment/Makefile	2011-05-02 18:41:07.506687972 +0200
+@@ -9,6 +9,6 @@
  install:
  	cp FlowgramAli_4frame ../bin/
  clean:

Modified: trunk/packages/denoiser/trunk/debian/patches/set_debian_path.patch
===================================================================
--- trunk/packages/denoiser/trunk/debian/patches/set_debian_path.patch	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/patches/set_debian_path.patch	2011-05-02 17:09:20 UTC (rev 6751)
@@ -1,18 +1,20 @@
---- Denoiser_0.851.orig/Denoiser/settings.py
-+++ Denoiser_0.851/Denoiser/settings.py
-@@ -8,7 +8,7 @@
+Index: Denoiser_0.91/Denoiser/settings.py
+===================================================================
+--- Denoiser_0.91.orig/Denoiser/settings.py	2011-03-10 07:05:48.000000000 +0100
++++ Denoiser_0.91/Denoiser/settings.py	2011-05-02 18:53:44.419668546 +0200
+@@ -7,7 +7,7 @@
  
- #see the INSTALL file for more details
+ home = environ['HOME']
  
 -PROJECT_HOME     = "" #This must be set to the install directory
 +PROJECT_HOME     = "/usr/share/denoiser" #This must be set to the install directory
  
- #specify the full path to python here if not in PATH 
+ #specify the full path to python here if not in PATH
  PYTHON_BIN       = "python"
-@@ -24,6 +24,6 @@
+@@ -22,6 +22,6 @@
+ DENOISE_WORKER   = PROJECT_HOME + "/Denoiser/denoise_worker.py" #Worker needed only on cluster
  
  SIGNAL_DIST_FILE = PROJECT_HOME + "/Data/probabilities.txt"
- LOOKUP           = PROJECT_HOME + "/Data/LookUp.dat"
 -FLOWGRAMALI      = PROJECT_HOME + "/bin/FlowgramAli_4frame"
 +FLOWGRAMALI      = "/usr/lib/denoiser/bin/FlowgramAli_4frame"
  

Modified: trunk/packages/denoiser/trunk/debian/rules
===================================================================
--- trunk/packages/denoiser/trunk/debian/rules	2011-05-02 15:42:25 UTC (rev 6750)
+++ trunk/packages/denoiser/trunk/debian/rules	2011-05-02 17:09:20 UTC (rev 6751)
@@ -14,6 +14,7 @@
 
 override_dh_clean:
 	$(MAKE) -C $(srcdir) clean
+	find . -name "*.dat" | xargs -r chmod -x
 	dh_clean
 
 get-orig-source:


