[med-svn] r16776 - in trunk/packages/mothur/trunk/debian: . patches
Timothy Booth
tbooth-guest at moszumanska.debian.org
Thu Apr 24 17:44:29 UTC 2014
Author: tbooth-guest
Date: 2014-04-24 17:44:28 +0000 (Thu, 24 Apr 2014)
New Revision: 16776
Added:
trunk/packages/mothur/trunk/debian/patches/find_pat_files
Modified:
trunk/packages/mothur/trunk/debian/changelog
trunk/packages/mothur/trunk/debian/control
trunk/packages/mothur/trunk/debian/get-orig-source
trunk/packages/mothur/trunk/debian/mothur.install
trunk/packages/mothur/trunk/debian/patches/makefile.patch
trunk/packages/mothur/trunk/debian/patches/series
trunk/packages/mothur/trunk/debian/rules
Log:
Add the important .pat files and tell Mothur how to find them (certainly not
in /usr/bin).
As usual ignore the changelog entry for the PPA build, this should work
with the -dfsg source used for Debian.
Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/changelog 2014-04-24 17:44:28 UTC (rev 16776)
@@ -1,3 +1,9 @@
+mothur (1.33.3+repack-0biolinux2) trusty; urgency=low
+
+ * Refresh patches and build for Ubuntu Trusty
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 24 Apr 2014 18:41:42 +0100
+
mothur (1.33.3+dfsg-1) unstable; urgency=medium
* New upstream version
@@ -38,6 +44,40 @@
-- Andreas Tille <tille at debian.org> Tue, 30 Jul 2013 14:32:44 +0200
+mothur (1.31.2+repack-0biolinux1) precise; urgency=low
+
+ * New upstream
+ * All patches look OK
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 16 Aug 2013 12:09:01 +0100
+
+mothur (1.30.2+repack-0ubuntu1) precise; urgency=low
+
+ * New upstream
+ * Drop unneeded patch from last time
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Apr 2013 11:56:20 +0100
+
+mothur (1.29.0+repack-0ubuntu1) precise; urgency=low
+
+ * New upstream for January
+ * Patch to fix compilation on MPI - not sure if it is right
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 15 Jan 2013 14:51:19 +0000
+
+mothur (1.28.0+repack-precise2) precise; urgency=low
+
+ * New upstream, build for precise
+ * Enable mpi for 32-bit, for completeness
+ * Note that this should really be version -0ubuntu2, but its
+ too late to go there
+ * Parallel build enabled
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 10 Jan 2013 15:22:35 +0000
+
+mothur (1.27.0+dfsg-1) UNRELEASED; urgency=low
+=======
+
mothur (1.27.0+repack-precise1) precise; urgency=low
* Remove -march=native from makefile as this makes the result
Modified: trunk/packages/mothur/trunk/debian/control
===================================================================
--- trunk/packages/mothur/trunk/debian/control 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/control 2014-04-24 17:44:28 UTC (rev 16776)
@@ -29,12 +29,12 @@
calculators and visualization tools were added.
Package: mothur-mpi
-Architecture: amd64
+Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
mothur,
openmpi-bin
Description: mpi-enabled binary for mothur
Provides the MPI-enabled binary for Mothur
- According to the docs this is of limited usefulness but is provided
- for completeness.
+ This is recommended for operations like shhh.flows which will be
+ very slow on a single processor.
Modified: trunk/packages/mothur/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/mothur/trunk/debian/get-orig-source 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/get-orig-source 2014-04-24 17:44:28 UTC (rev 16776)
@@ -1,9 +1,10 @@
#!/bin/sh
# script to download and repack source package of mothur because it is provided as zip
+# This is broken
# set -x
PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download | \
+VERSION=`env USCAN_REPACK= uscan --verbose --force-download | \
grep "Newest version on remote site is .* local version is .*" | \
head -n 1 | \
sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
@@ -20,5 +21,5 @@
find ${UPSTREAMDIR} -name ".*" | xargs rm -f
find ${UPSTREAMDIR} -name "*.o" | xargs rm -f
+rm -rf "${UPSTREAMDIR}" __MACOSX
XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -caf "$PKG"_"$VERSION".orig.tar.xz "${UPSTREAMDIR}"
-rm -rf "${UPSTREAMDIR}" __MACOSX
Modified: trunk/packages/mothur/trunk/debian/mothur.install
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur.install 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/mothur.install 2014-04-24 17:44:28 UTC (rev 16776)
@@ -1,2 +1,3 @@
mothur /usr/bin
uchime /usr/bin
+lookupFiles/* /usr/share/mothur
Added: trunk/packages/mothur/trunk/debian/patches/find_pat_files
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/find_pat_files (rev 0)
+++ trunk/packages/mothur/trunk/debian/patches/find_pat_files 2014-04-24 17:44:28 UTC (rev 16776)
@@ -0,0 +1,49 @@
+Mothur ships with some .pat files which are needed by a couple of commands.
+Default behaviour is to fall back to looking in the exec dir, which makes
+no sense in a package, so redirect it.
+--- a/shhhercommand.cpp
++++ b/shhhercommand.cpp
+@@ -314,10 +314,10 @@
+ for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+
+- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
+- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
++ string tryPath = "/usr/share/mothur/";
++ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
++ ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
+ in2.close();
+ lookupFileName = tryPath;
+ }
+@@ -334,10 +334,10 @@
+ for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+
+- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
+- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
++ string tryPath = "/usr/share/mothur/";
++ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+- int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
++ int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
+ in2.close();
+ lookupFileName = tryPath;
+
+--- a/sffmultiplecommand.cpp
++++ b/sffmultiplecommand.cpp
+@@ -315,10 +315,10 @@
+ for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+
+- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
+- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
++ string tryPath = "/usr/share/mothur/";
++ m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+- int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
++ int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
+ in2.close();
+ lookupFileName = tryPath;
+
Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch 2014-04-24 17:44:28 UTC (rev 16776)
@@ -9,8 +9,8 @@
# Optimize to level 3:
-CXXFLAGS += -O3
-+# Nope, let debuild set this.
-+# CXXFLAGS += -O3
++# Nope - let debuild set this
++#CXXFLAGS += -O3
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are using centos uncomment the following lines
@@ -28,7 +28,7 @@
#CXXFLAGS += -mtune=native -march=native
+ # But not if you are trying to make a generic build for
+ # packaging, because your binary will end up being specific
-+ # to your processor.
++ # to your own processor.
CXXFLAGS += -DBIT_VERSION
- FORTRAN_FLAGS = -m64
Modified: trunk/packages/mothur/trunk/debian/patches/series
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/series 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/patches/series 2014-04-24 17:44:28 UTC (rev 16776)
@@ -4,5 +4,6 @@
catchall_fix.patch
build_without_tty.patch
uchime_link_dynamically
+find_pat_files
uchime_hardening.patch
spelling.patch
Modified: trunk/packages/mothur/trunk/debian/rules
===================================================================
--- trunk/packages/mothur/trunk/debian/rules 2014-04-24 16:28:58 UTC (rev 16775)
+++ trunk/packages/mothur/trunk/debian/rules 2014-04-24 17:44:28 UTC (rev 16776)
@@ -6,17 +6,20 @@
#export DH_VERBOSE=1
ARCHBITS ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
+THREADS ?= -j3
%:
dh $@
override_dh_auto_build:
if [ $(ARCHBITS) -eq 64 ] ; then \
- dh_auto_build -- 64BIT_VERSION=yes USEMPI=yes && \
+ dh_auto_build -- $(THREADS) 64BIT_VERSION=yes USEMPI=yes && \
mv mothur mothur-mpi && make clean && \
- dh_auto_build -- 64BIT_VERSION=yes USEMPI=no ; \
+ dh_auto_build -- $(THREADS) 64BIT_VERSION=yes USEMPI=no ; \
else \
- dh_auto_build -- 64BIT_VERSION=no ; \
+ dh_auto_build -- $(THREADS) 64BIT_VERSION=no USEMPI=yes && \
+ mv mothur mothur-mpi && make clean && \
+ dh_auto_build -- $(THREADS) 64BIT_VERSION=no USEMPI=no ; \
fi
override_dh_auto_install:
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