[med-svn] r7251 - in trunk/packages/ampliconnoise/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Mon Jul 11 16:34:30 UTC 2011
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 <tbooth at ceh.ac.uk> Thu, 07 Jul 2011 17:39:42 +0100
+
+ampliconnoise (1.24-1ubuntu1) lucid; urgency=low
+
+ * New upstream
+
+ -- Tim Booth <tbooth at ceh.ac.uk> 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 <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>, Steffen Moeller <moeller at debian.org>
-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
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