[med-svn] r12066 - in trunk/packages/mothur/trunk/debian: . patches

Wed Aug 15 15:25:36 UTC 2012

Author: tbooth-guest
Date: 2012-08-15 15:25:36 +0000 (Wed, 15 Aug 2012)
New Revision: 12066

Added:
   trunk/packages/mothur/trunk/debian/mothur-mpi.install
   trunk/packages/mothur/trunk/debian/mothur.install
Modified:
   trunk/packages/mothur/trunk/debian/changelog
   trunk/packages/mothur/trunk/debian/compat
   trunk/packages/mothur/trunk/debian/control
   trunk/packages/mothur/trunk/debian/install
   trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
   trunk/packages/mothur/trunk/debian/patches/makefile.patch
   trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
   trunk/packages/mothur/trunk/debian/patches/series
   trunk/packages/mothur/trunk/debian/rules
Log:
Updated for the latest Mothur (only tested on Ubuntu)



Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================

--- trunk/packages/mothur/trunk/debian/changelog	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/changelog	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1,3 +1,30 @@
+mothur (1.27.0+repack-precise1) precise; urgency=low
+
+  * New minor release from upstream
+  * Build MPI version alongside regular version
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 14 Aug 2012 18:46:58 +0100
+
+mothur (1.25.0~repack-lucid3) lucid; urgency=low
+
+  * Removed dependency on catchall - this belongs in the
+    bio-linux-mothur package.  Not sure what I was thinking there.
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Mon, 14 May 2012 10:57:22 +0100
+
+mothur (1.25.0~repack-lucid2) lucid; urgency=low
+
+  * Fix 32-bit build and add uchime (which should be packaged
+    separately, but I've no time for that just now)
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 10 May 2012 10:43:04 +0100
+
+mothur (1.25.0~repack-lucid1) lucid; urgency=low
+
+  * Rebuild for Lucid with repack fudge again
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 09 May 2012 11:20:15 +0100
+
 mothur (1.25.0-1) UNRELEASED; urgency=low
 
   * New upstream release

Modified: trunk/packages/mothur/trunk/debian/compat
===================================================================
--- trunk/packages/mothur/trunk/debian/compat	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/compat	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1 +1 @@
-9
+8

Modified: trunk/packages/mothur/trunk/debian/control
===================================================================
--- trunk/packages/mothur/trunk/debian/control	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/control	2012-08-15 15:25:36 UTC (rev 12066)
@@ -5,7 +5,7 @@
 Uploaders: Steffen Moeller <moeller at debian.org>,
  Andreas Tille <tille at debian.org>,
  Tim Booth <tbooth at ceh.ac.uk>
-Build-Depends: debhelper (>= 9), libreadline-dev, gfortran
+Build-Depends: debhelper (>= 8), libreadline-dev, gfortran, quilt, libopenmpi-dev
 Standards-Version: 3.9.3
 Homepage: http://www.mothur.org
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mothur/trunk/
@@ -14,6 +14,8 @@
 Package: mothur
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Provides: uchime
+Conflicts: uchime
 Description: sequence analysis suite for research on microbiota
  Mothur seeks to develop a single piece of open-source, expandable
  software to fill the bioinformatics needs of the microbial ecology
@@ -21,3 +23,11 @@
  treeclimber, s-libshuff, unifrac, and much more. In addition to improving
  the flexibility of these algorithms, a number of other features including
  calculators and visualization tools were added.
+
+Package: mothur-mpi
+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

Modified: trunk/packages/mothur/trunk/debian/install
===================================================================
--- trunk/packages/mothur/trunk/debian/install	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/install	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1 +1,3 @@
 mothur /usr/bin
+mothurMPI /usr/bin
+uchime /usr/bin

Added: trunk/packages/mothur/trunk/debian/mothur-mpi.install
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur-mpi.install	                        (rev 0)
+++ trunk/packages/mothur/trunk/debian/mothur-mpi.install	2012-08-15 15:25:36 UTC (rev 12066)
@@ -0,0 +1 @@
+mothur-mpi /usr/bin

Added: trunk/packages/mothur/trunk/debian/mothur.install
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur.install	                        (rev 0)
+++ trunk/packages/mothur/trunk/debian/mothur.install	2012-08-15 15:25:36 UTC (rev 12066)
@@ -0,0 +1,2 @@
+mothur /usr/bin
+uchime /usr/bin

Modified: trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch	2012-08-15 15:25:36 UTC (rev 12066)
@@ -2,8 +2,8 @@
 Date: Thu, 10 Nov 2011 00:39:01 UTC
 Closes: #648255
 Description: Fix for FTBFS: cc1plus: error: unrecognized command line option '-msse2'
---- mothur-1.24.1.orig/uchime_src/mk
-+++ mothur-1.24.1/uchime_src/mk
+--- a/uchime_src/mk
++++ b/uchime_src/mk
 @@ -7,7 +7,7 @@
  for CPPName in $CPPNames
  do

Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1,7 +1,7 @@
 Author: Steffen Moeller <moeller at debian.org>
 Purpose: Comment MAC specific option
---- mothur-1.24.1.orig/makefile
-+++ mothur-1.24.1/makefile
+--- a/makefile
++++ b/makefile
 @@ -28,7 +28,7 @@
  	#CXX = g++44
  	
@@ -11,3 +11,12 @@
  	
  	#if you using cygwin to build Windows the following line
  	#CXX = x86_64-w64-mingw32-g++
+@@ -37,7 +37,7 @@
+  	#TARGET_ARCH += -m64 -static
+ 
+ 	#if you are a linux user use the following line
+-	#CXXFLAGS += -mtune=native -march=native -m64
++	CXXFLAGS += -mtune=native -march=native -m64
+ 	
+ 	CXXFLAGS += -DBIT_VERSION 
+     	FORTRAN_FLAGS = -m64

Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1,8 +1,8 @@
 Author: Andreas Tille <tille at debian.org>
 Date: 2011-01-30
 Dscription: There is no need to link against lncurses because its symbols are not used
---- mothur-1.24.1.orig/makefile
-+++ mothur-1.24.1/makefile
+--- a/makefile
++++ b/makefile
 @@ -63,8 +63,7 @@
  ifeq  ($(strip $(USEREADLINE)),yes)
      CXXFLAGS += -DUSE_READLINE

Modified: trunk/packages/mothur/trunk/debian/patches/series
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/series	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/patches/series	2012-08-15 15:25:36 UTC (rev 12066)
@@ -1,3 +1,6 @@
 makefile.patch
 no_lcurses.patch
 drop_sse_option.patch
+catchall_fix.patch
+build_without_tty.patch
+uchime_link_dynamically

Modified: trunk/packages/mothur/trunk/debian/rules
===================================================================
--- trunk/packages/mothur/trunk/debian/rules	2012-08-15 11:53:40 UTC (rev 12065)
+++ trunk/packages/mothur/trunk/debian/rules	2012-08-15 15:25:36 UTC (rev 12066)
@@ -8,23 +8,25 @@
 ARCHBITS ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
 
 %:
-	dh $@
+	dh $@ --with quilt
 
 override_dh_auto_build:
 	if [ $(ARCHBITS) -eq 64 ] ; then \
-	    dh_auto_build 64BIT_VERSION=yes ; \
+	    dh_auto_build -- 64BIT_VERSION=yes USEMPI=yes && \
+	    mv mothur mothur-mpi && make clean && \
+	    dh_auto_build -- 64BIT_VERSION=yes USEMPI=no ; \
 	else \
-	    dh_auto_build ; \
+	    dh_auto_build -- 64BIT_VERSION=no ; \
 	fi
 
 override_dh_auto_install:
-	dh_install
+	true
 
 get-orig-source:
 	. debian/get-orig-source
 
 #Cleaning needs help right now
 override_dh_auto_clean:
-	rm -f mothur *.o
+	rm -f mothur mothur-mpi *.o mothur.*.logfile
 	make clean
 	( cd uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr )


