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 <[email protected]> Mon, 02 May 2011 18:03:45 +0200 + +denoiser (0.8.5.1-1) UNRELEASED; urgency=low + + * Initial release. + -- Andreas Tille <[email protected]> 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 <[email protected]> -Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, - Steffen Moeller <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), python-support, python, ghc6 -Standards-Version: 3.9.1 +Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> +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: _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
