Author: tbooth-guest Date: 2011-07-11 16:34:29 +0000 (Mon, 11 Jul 2011) New Revision: 7251
Modified: trunk/packages/ampliconnoise/trunk/debian/changelog trunk/packages/ampliconnoise/trunk/debian/control trunk/packages/ampliconnoise/trunk/debian/get-orig-source trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch trunk/packages/ampliconnoise/trunk/debian/rules Log: Change to use openmpi instead of mpich2 (though the build was in fact ambiguous!) and other fixups. Modified: trunk/packages/ampliconnoise/trunk/debian/changelog =================================================================== --- trunk/packages/ampliconnoise/trunk/debian/changelog 2011-07-11 15:52:48 UTC (rev 7250) +++ trunk/packages/ampliconnoise/trunk/debian/changelog 2011-07-11 16:34:29 UTC (rev 7251) @@ -1,3 +1,17 @@ +ampliconnoise (1.24-1ubuntu2) lucid; urgency=low + + * Fix build to use OpenMPI explicitly. Explicitly made build use + mpicc.openmpi even if MPICH2 is installed and set as default. + * More tweaks to ugly tarball repacking. + + -- Tim Booth <[email protected]> Thu, 07 Jul 2011 17:39:42 +0100 + +ampliconnoise (1.24-1ubuntu1) lucid; urgency=low + + * New upstream + + -- Tim Booth <[email protected]> Fri, 20 May 2011 17:04:15 +0100 + ampliconnoise (1.22-2) unstable; urgency=low * Initial upload (Closes: #624362). Modified: trunk/packages/ampliconnoise/trunk/debian/control =================================================================== --- trunk/packages/ampliconnoise/trunk/debian/control 2011-07-11 15:52:48 UTC (rev 7250) +++ trunk/packages/ampliconnoise/trunk/debian/control 2011-07-11 16:34:29 UTC (rev 7251) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Tim Booth <[email protected]>, Andreas Tille <[email protected]>, Steffen Moeller <[email protected]> -Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7.1~), libgsl0-dev, libmpich2-dev (>= 1.2) +Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7.1~), libgsl0-dev, libopenmpi-dev (>= 1.4) Standards-Version: 3.9.2 Homepage: http://code.google.com/p/ampliconnoise/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ampliconnoise/trunk/?rev=0&sc=0 @@ -13,7 +13,7 @@ Package: ampliconnoise Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libgsl0ldbl, mafft -Recommends: mpi-default-bin +Recommends: openmpi-bin Description: Programs for the removal of noise from 454 sequenced PCR amplicons AmpliconNoise is a package of applications to clean up high-throughput sequence data. It consists of three main parts: Modified: trunk/packages/ampliconnoise/trunk/debian/get-orig-source =================================================================== --- trunk/packages/ampliconnoise/trunk/debian/get-orig-source 2011-07-11 15:52:48 UTC (rev 7250) +++ trunk/packages/ampliconnoise/trunk/debian/get-orig-source 2011-07-11 16:34:29 UTC (rev 7251) @@ -25,7 +25,10 @@ find . -name "${UPSTREAMNAME}V${VERSION}" -type d | xargs -r rm -r tar -xzf ${UPSTREAMNAME}V${VERSION}.tar.gz find ${UPSTREAMNAME}V${VERSION} -name .svn -type d | xargs -r rm -rf +find ${UPSTREAMNAME}V${VERSION} -name '._*' | xargs -r rm -rf find . -name "ampliconnoise_*.orig.tar.gz" -type l | xargs -r rm GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz ${UPSTREAMNAME}V${VERSION} find . -name "${UPSTREAMNAME}V${VERSION}" -type d | xargs -r rm -r + +cp *.orig.tar.gz .. Modified: trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch =================================================================== --- trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch 2011-07-11 15:52:48 UTC (rev 7250) +++ trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch 2011-07-11 16:34:29 UTC (rev 7251) @@ -9,10 +9,8 @@ A better fix would be to allow setting of the Data directory via an environment variable or a variable passed to MAKE at build time. This could be contributed back to upstream. -Index: AmpliconNoiseV1.22/SeqNoise/SeqNoise.h -=================================================================== ---- AmpliconNoiseV1.22.orig/SeqNoise/SeqNoise.h 2011-05-03 11:46:15.574549909 +0200 -+++ AmpliconNoiseV1.22/SeqNoise/SeqNoise.h 2011-05-03 11:46:30.442415391 +0200 +--- a/SeqNoise/SeqNoise.h ++++ b/SeqNoise/SeqNoise.h @@ -113,7 +113,7 @@ /********DEFAULTS***********/ #define DEF_SIGMA 30.0 @@ -22,10 +20,8 @@ /***************************/ /******Programming Constants************/ -Index: AmpliconNoiseV1.22/SeqDistM/SeqDistM.h -=================================================================== ---- AmpliconNoiseV1.22.orig/SeqDistM/SeqDistM.h 2011-05-03 11:46:15.582549837 +0200 -+++ AmpliconNoiseV1.22/SeqDistM/SeqDistM.h 2011-05-03 11:46:30.442415391 +0200 +--- a/SeqDistM/SeqDistM.h ++++ b/SeqDistM/SeqDistM.h @@ -71,7 +71,7 @@ /* User defined structures */ @@ -35,10 +31,8 @@ typedef struct s_Align -Index: AmpliconNoiseV1.22/SeqDist/SeqDist.h -=================================================================== ---- AmpliconNoiseV1.22.orig/SeqDist/SeqDist.h 2011-05-03 11:46:15.558550053 +0200 -+++ AmpliconNoiseV1.22/SeqDist/SeqDist.h 2011-05-03 11:46:30.442415391 +0200 +--- a/SeqDist/SeqDist.h ++++ b/SeqDist/SeqDist.h @@ -71,7 +71,7 @@ /* User defined structures */ @@ -48,10 +42,8 @@ typedef struct s_Align -Index: AmpliconNoiseV1.22/SeqNoiseM/SeqNoiseM.h -=================================================================== ---- AmpliconNoiseV1.22.orig/SeqNoiseM/SeqNoiseM.h 2011-05-03 11:46:15.546550163 +0200 -+++ AmpliconNoiseV1.22/SeqNoiseM/SeqNoiseM.h 2011-05-03 11:46:30.442415391 +0200 +--- a/SeqNoiseM/SeqNoiseM.h ++++ b/SeqNoiseM/SeqNoiseM.h @@ -113,7 +113,7 @@ /********DEFAULTS***********/ #define DEF_SIGMA 30.0 @@ -61,10 +53,8 @@ /***************************/ /******Programming Constants************/ -Index: AmpliconNoiseV1.22/PyroNoiseM/PyroNoiseM.h -=================================================================== ---- AmpliconNoiseV1.22.orig/PyroNoiseM/PyroNoiseM.h 2011-05-03 11:46:15.554550089 +0200 -+++ AmpliconNoiseV1.22/PyroNoiseM/PyroNoiseM.h 2011-05-03 11:46:30.442415391 +0200 +--- a/PyroNoiseM/PyroNoiseM.h ++++ b/PyroNoiseM/PyroNoiseM.h @@ -36,7 +36,7 @@ #define OVERCALL_THRESH 6.0 /*?*/ @@ -74,10 +64,8 @@ #define OUT_FILE_STUB "-out" #define INIT_FILE "-lin" -Index: AmpliconNoiseV1.22/PyroNoise/PyroNoise.h -=================================================================== ---- AmpliconNoiseV1.22.orig/PyroNoise/PyroNoise.h 2011-05-03 11:46:15.538550235 +0200 -+++ AmpliconNoiseV1.22/PyroNoise/PyroNoise.h 2011-05-03 11:46:30.446415355 +0200 +--- a/PyroNoise/PyroNoise.h ++++ b/PyroNoise/PyroNoise.h @@ -37,7 +37,7 @@ #define OVERCALL_THRESH 6.0 /*?*/ @@ -87,11 +75,9 @@ #define OUT_FILE_STUB "-out" #define INIT_FILE "-lin" -Index: AmpliconNoiseV1.22/Perseus/Perseus.h -=================================================================== ---- AmpliconNoiseV1.22.orig/Perseus/Perseus.h 2011-05-03 11:46:15.566549981 +0200 -+++ AmpliconNoiseV1.22/Perseus/Perseus.h 2011-05-03 11:46:30.446415355 +0200 -@@ -86,7 +86,7 @@ +--- a/Perseus/Perseus.h ++++ b/Perseus/Perseus.h +@@ -90,7 +90,7 @@ #define WEIGHTDELIM '_' #define N_BASES 4 @@ -100,10 +86,8 @@ #ifndef min #define min(x, y) ((x) < (y) ? (x) : (y)) -Index: AmpliconNoiseV1.22/PyroDist/PyroDist.h -=================================================================== ---- AmpliconNoiseV1.22.orig/PyroDist/PyroDist.h 2011-05-03 11:46:15.530550307 +0200 -+++ AmpliconNoiseV1.22/PyroDist/PyroDist.h 2011-05-03 11:46:30.446415355 +0200 +--- a/PyroDist/PyroDist.h ++++ b/PyroDist/PyroDist.h @@ -34,7 +34,7 @@ #define LEFT 1 #define UP 2 Modified: trunk/packages/ampliconnoise/trunk/debian/rules =================================================================== --- trunk/packages/ampliconnoise/trunk/debian/rules 2011-07-11 15:52:48 UTC (rev 7250) +++ trunk/packages/ampliconnoise/trunk/debian/rules 2011-07-11 16:34:29 UTC (rev 7251) @@ -4,8 +4,17 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +# Set source directory - stray . file in root of tarball stops it +# unpacking cleanly. Sadly this deosn't help Quilt +# so I repack the tarball instead. +# SOURCEDIR := $(shell echo AmpliconNoise*) + +# Override path as a way to hook mpicc +PATH := $(CURDIR)/debian/bin_override:${PATH} +export PATH + %: - dh --with quilt $@ + dh --with quilt $@ override_dh_auto_install: make install _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
