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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]>, Tim Booth <[email protected]> -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 $CPPNames do Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-08-15 11:53:40 UTC (rev 12065) +++ trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-08-15 15:25:36 UTC (rev 12066) @@ -1,7 +1,7 @@ Author: Steffen Moeller <[email protected]> Purpose: Comment MAC specific option ---- mothur-1.24.1.orig/makefile -+++ mothur-1.24.1/makefile +--- a/makefile ++++ b/makefile @@ -28,7 +28,7 @@ #CXX = g++44 @@ -11,3 +11,12 @@ #if you using cygwin to build Windows the following line #CXX = x86_64-w64-mingw32-g++ +@@ -37,7 +37,7 @@ + #TARGET_ARCH += -m64 -static + + #if you are a linux user use the following line +- #CXXFLAGS += -mtune=native -march=native -m64 ++ CXXFLAGS += -mtune=native -march=native -m64 + + CXXFLAGS += -DBIT_VERSION + FORTRAN_FLAGS = -m64 Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-08-15 11:53:40 UTC (rev 12065) +++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-08-15 15:25:36 UTC (rev 12066) @@ -1,8 +1,8 @@ Author: Andreas Tille <[email protected]> Date: 2011-01-30 Dscription: There is no need to link against lncurses because its symbols are not used ---- mothur-1.24.1.orig/makefile -+++ mothur-1.24.1/makefile +--- a/makefile ++++ b/makefile @@ -63,8 +63,7 @@ ifeq ($(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 ) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
