Author: moeller Date: 2013-07-25 14:11:24 +0000 (Thu, 25 Jul 2013) New Revision: 14238
Added: trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch Removed: trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base trunk/packages/hhsuite/trunk/debian/patches/hardening Modified: trunk/packages/hhsuite/trunk/debian/changelog trunk/packages/hhsuite/trunk/debian/control trunk/packages/hhsuite/trunk/debian/hhsuite-data.install trunk/packages/hhsuite/trunk/debian/hhsuite-data.links trunk/packages/hhsuite/trunk/debian/hhsuite.docs trunk/packages/hhsuite/trunk/debian/hhsuite.install trunk/packages/hhsuite/trunk/debian/hhsuite.links trunk/packages/hhsuite/trunk/debian/patches/rest1 trunk/packages/hhsuite/trunk/debian/patches/series Log: Merged own attempt to package hhsuite 2.0.16 with the one of Laszlo ... sorry, I did not look right. A noticable change may be the scripts directory, which moved from the hhuite-data directory hhsuite itself. Laslo - is that fine with you? Also, a new hhsuite-doc package now separates the user guide from the binaries. Modified: trunk/packages/hhsuite/trunk/debian/changelog =================================================================== --- trunk/packages/hhsuite/trunk/debian/changelog 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/changelog 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,13 +1,20 @@ hhsuite (2.0.16-2) UNRELEASED; urgency=low - * NOT RELEASED YET + [Steffen Moeller] + * Bumped standard to 3.9.4. + * Removed DMUA flag. + * Created new -doc package and moved user guide to it + * Moved scripts directory from hhsuite-data to hhsuite + * Added CHANGES file to .docs + * joined hardening patch with rest1 - -- Laszlo Kajan <[email protected]> Tue, 28 May 2013 10:01:03 +0200 + -- Steffen Moeller <[email protected]> Thu, 25 Jul 2013 16:05:49 +0200 hhsuite (2.0.16-1) unstable; urgency=low + [Laszlo Kajan] * New upstream release. - * Updated d/watch file. + * Updated debian/watch file. -- Laszlo Kajan <[email protected]> Mon, 24 Sep 2012 09:32:14 +0200 Modified: trunk/packages/hhsuite/trunk/debian/control =================================================================== --- trunk/packages/hhsuite/trunk/debian/control 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/control 2013-07-25 14:11:24 UTC (rev 14238) @@ -4,11 +4,10 @@ Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Laszlo Kajan <[email protected]> Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://toolkit.genzentrum.lmu.de/sections/search Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/ -DM-Upload-Allowed: yes Package: hhsuite Architecture: amd64 @@ -33,6 +32,13 @@ HHblits is faster, up to twice as sensitive and produces more accurate alignments. +Package: hhsuite-doc +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: hhsuite +Description: documentation for HHsuite for HMM-HMM comparisons + This package provides a PDF with the user guide for the HH-suite. + Package: hhsuite-data Architecture: all Depends: ${misc:Depends} Modified: trunk/packages/hhsuite/trunk/debian/hhsuite-data.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite-data.install 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.install 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,2 +1 @@ usr/share/hhsuite/data -usr/share/hhsuite/scripts Modified: trunk/packages/hhsuite/trunk/debian/hhsuite-data.links =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite-data.links 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.links 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,3 +1,2 @@ -usr/share/hhsuite/scripts usr/lib/hhsuite/scripts usr/share/hhsuite/data/context_data.lib usr/lib/hhsuite/data/context_data.lib usr/share/hhsuite/data/cs219.lib usr/lib/hhsuite/data/cs219.lib Copied: trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base (from rev 13047, trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base) =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base (rev 0) +++ trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base 2013-07-25 14:11:24 UTC (rev 14238) @@ -0,0 +1,8 @@ +Document: hhsuite +Title: HH-suite User Guide +Author: Johannes Söding, Michael Remmert, Andreas Hauser +Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz Added: trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs (rev 0) +++ trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs 2013-07-25 14:11:24 UTC (rev 14238) @@ -0,0 +1 @@ +hhsuite-userguide.pdf Deleted: trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,8 +0,0 @@ -Document: hhsuite -Title: HH-suite User Guide -Author: Johannes Söding, Michael Remmert, Andreas Hauser -Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment. -Section: Science/Biology - -Format: PDF -Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.docs =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.docs 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.docs 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,2 +1,2 @@ -hhsuite-userguide.pdf README +CHANGES Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.install 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.install 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,3 +1,4 @@ usr/bin/hh* usr/lib/hhsuite/bin usr/lib/hhsuite/data +usr/share/hhsuite/scripts Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.links =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.links 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.links 2013-07-25 14:11:24 UTC (rev 14238) @@ -1 +1,2 @@ -/usr/lib/hhsuite usr/lib/hh +usr/share/hhsuite/scripts usr/lib/hhsuite/scripts +usr/lib/hhsuite usr/lib/hh Added: trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch (rev 0) +++ trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch 2013-07-25 14:11:24 UTC (rev 14238) @@ -0,0 +1,16 @@ +Index: hhsuite-2.0.16/data/Makefile +=================================================================== +--- /dev/null ++++ hhsuite-2.0.16/data/Makefile +@@ -0,0 +1,11 @@ ++#!/usr/bin/make -f ++ ++DUMMYDB:=do_not_delete.phr do_not_delete.pin do_not_delete.psq ++ ++all: $(DUMMYDB) ++ ++%.phr %.pin %.psq : % ++ formatdb -i '$<' && rm -f formatdb.log ++ ++clean: ++ rm -f $(DUMMYDB) formatdb.log Deleted: trunk/packages/hhsuite/trunk/debian/patches/hardening =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/hardening 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/patches/hardening 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,22 +0,0 @@ -Description: Hardening patch. -Author: Laszlo Kajan <[email protected]> ---- a/src/Makefile -+++ b/src/Makefile -@@ -20,7 +20,7 @@ - OBJECT_LIBS = -openmp - else # ifndef ICC - CXX = g++ -- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp -+ CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp - HHSEARCH_LIBS = -lpthread - HHBLITS_LIBS = -lpthread -fopenmp - HHALIGN_LIBS = -@@ -51,7 +51,7 @@ - endif - endif # ifndef ICC - --CPP = $(CXX) $(CXXFLAGS) -+CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) - CPP_VALGRIND = $(CXX) -g $(CXXFLAGS) - - Modified: trunk/packages/hhsuite/trunk/debian/patches/rest1 =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/rest1 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/patches/rest1 2013-07-25 14:11:24 UTC (rev 14238) @@ -1,24 +1,36 @@ Description: Assorted patches + * Set paths to hhsuite components for Perl scripts. * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq . Author: Laszlo Kajan <[email protected]> ---- a/src/Makefile -+++ b/src/Makefile +Index: hhsuite-2.0.16/src/Makefile +=================================================================== +--- hhsuite-2.0.16.orig/src/Makefile ++++ hhsuite-2.0.16/src/Makefile @@ -14,13 +14,13 @@ ifdef ICC CXX = env LANG=C icc - CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) -I$(FFINDEX_DIR) -+ CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) ++ CXXFLAGS += -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) HHSEARCH_LIBS = -lpthread -lrt HHBLITS_LIBS = -lpthread -lrt -openmp OBJECT_LIBS = -openmp else # ifndef ICC CXX = g++ - CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -fopenmp -+ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp ++ CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp HHSEARCH_LIBS = -lpthread HHBLITS_LIBS = -lpthread -fopenmp HHALIGN_LIBS = +@@ -51,7 +51,7 @@ + endif + endif # ifndef ICC + +-CPP = $(CXX) $(CXXFLAGS) ++CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) + CPP_VALGRIND = $(CXX) -g $(CXXFLAGS) + + @@ -92,7 +92,7 @@ $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS) @@ -28,17 +40,3 @@ hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS) $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a ---- /dev/null -+++ b/data/Makefile -@@ -0,0 +1,11 @@ -+#!/usr/bin/make -f -+ -+DUMMYDB:=do_not_delete.phr do_not_delete.pin do_not_delete.psq -+ -+all: $(DUMMYDB) -+ -+%.phr %.pin %.psq : % -+ formatdb -i '$<' && rm -f formatdb.log -+ -+clean: -+ rm -f $(DUMMYDB) formatdb.log Modified: trunk/packages/hhsuite/trunk/debian/patches/series =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/series 2013-07-25 14:10:10 UTC (rev 14237) +++ trunk/packages/hhsuite/trunk/debian/patches/series 2013-07-25 14:11:24 UTC (rev 14238) @@ -3,8 +3,8 @@ help rest1 perlscript_uselib -hardening unused_variables_warning unnecessary_libz perl_interpreter version_bump +add_Makefile_in_data.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
