Commit 08212f49 authored by Tim Booth's avatar Tim Booth
Browse files

Committing various tweaks made for Bio-Linux but relevant for Debian. 

The most important change is that the makefile definitely shouldn't 
have "-march=native" as it enables optimisations specific to the build
machine and potentially incompatible with other CPUs.
parent e3ddcbdf

debian/changelog

+10 −1
Original line number Diff line number Diff line
@@ -9,10 +9,19 @@ 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

    depend on the build machine - so a package built on a Core3

    CPU won't work on a Xeon.



 -- Tim Booth <tbooth@ceh.ac.uk>  Fri, 12 Oct 2012 11:41:04 +0100



mothur (1.27.0+repack-precise2) precise; urgency=low



  * New minor release from upstream

  * Build MPI version alongside regular version

  * ...but only for 64-bit



 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 14 Aug 2012 18:46:58 +0100

 -- Tim Booth <tbooth@ceh.ac.uk>  Wed, 10 Oct 2012 11:20:43 +0100



mothur (1.25.0~repack-lucid3) lucid; urgency=low

debian/control

+2 −2
Original line number Diff line number Diff line
@@ -25,9 +25,9 @@ Description: sequence analysis suite for research on microbiota 
 calculators and visualization tools were added.



Package: mothur-mpi

Architecture: any

Architecture: amd64

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
 
 for completeness.

debian/patches/build_without_tty.patch

0 → 100644
+11 −0
Original line number Diff line number Diff line 
--- a/uchime_src/mk

+++ b/uchime_src/mk

@@ -6,7 +6,7 @@

 

 for CPPName in $CPPNames

 do

-  echo $CPPName >> /dev/tty

+  echo $CPPName >&2

   g++ $ENV_GCC_OPTS -c -O2 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o  >> mk.stdout 2>> tmp.stderr

 	cat tmp.stderr

 	cat tmp.stderr >> mk.stderr

debian/patches/catchall_fix.patch

0 → 100644
+26 −0
Original line number Diff line number Diff line 
This removes a workaround that is better fixed in Catchall than in

Mothur, so I did that (packaged in bio-linux-catchall just now as I

don't have the source compiling yet.)



--- a/catchallcommand.cpp

+++ b/catchallcommand.cpp

@@ -190,6 +190,7 @@

 		

 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}

 		

+		/* TB for Bio-Linux: Don't need this...

 		//get location of catchall

 		path = m->argv;

 		path = path.substr(0, (path.find_last_of("othur")-5));

@@ -238,6 +239,11 @@

         

 		//prepare full output directory

 		outputDir = m->getFullPathName(outputDir);

+		*/

+

+		/* TB for Bio-Linux: We just need this, assuming catchall is properly wrapped to avoid

+		 * the bug described above - see the bio-linux-catchall package */

+		string catchAllCommandExe = "catchall ";

 		

         if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }

debian/patches/makefile.patch

+23 −6
Original line number Diff line number Diff line 
Author: Steffen Moeller <moeller@debian.org>

Author: Steffen Moeller <moeller@debian.org>, Tim Booth <tbooth@ceh.ac.uk>

Purpose: Comment MAC specific option

  Set -m64 but not -march=native for 64-bit build

--- a/makefile

+++ b/makefile

@@ -28,7 +28,7 @@

@@ -21,14 +21,15 @@

 FORTRAN_FLAGS = 

 

 # Optimize to level 3:

-CXXFLAGS += -O3 

+# Nope, let debuild set this.

+# CXXFLAGS += -O3

 

 ifeq  ($(strip $(64BIT_VERSION)),yes)

 	#if you are using centos uncomment the following lines

 	#CXX = g++44

 	

 	#if you are a mac user use the following line
@@ -11,12 +21,19 @@ Purpose: Comment MAC specific option 
 	

 	#if you using cygwin to build Windows the following line

 	#CXX = x86_64-w64-mingw32-g++

@@ -37,7 +37,7 @@

  	#TARGET_ARCH += -m64 -static

@@ -38,6 +39,10 @@

 

 	#if you are a linux user use the following line

-	#CXXFLAGS += -mtune=native -march=native -m64

+	CXXFLAGS += -mtune=native -march=native -m64

 	#CXXFLAGS += -mtune=native -march=native -m64

+	# But not if you are trying to make a generic build for

+	# packaging, because your binary will end up being specific

+	# to your processor.

+	CXXFLAGS += -m64

 	

 	CXXFLAGS += -DBIT_VERSION 

     	FORTRAN_FLAGS = -m64

@@ -120,4 +125,3 @@

 clean :

 	@rm -f $(OBJECTS)

 	@rm -f uchime

-