Author: lkajan-guest Date: 2012-01-20 21:02:42 +0000 (Fri, 20 Jan 2012) New Revision: 9354
Added: trunk/packages/hhsuite/trunk/ trunk/packages/hhsuite/trunk/debian/ trunk/packages/hhsuite/trunk/debian/README.source trunk/packages/hhsuite/trunk/debian/changelog trunk/packages/hhsuite/trunk/debian/compat trunk/packages/hhsuite/trunk/debian/control trunk/packages/hhsuite/trunk/debian/copyright trunk/packages/hhsuite/trunk/debian/docs trunk/packages/hhsuite/trunk/debian/ffindex.install trunk/packages/hhsuite/trunk/debian/hhsuite.install trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install trunk/packages/hhsuite/trunk/debian/libffindex0.install trunk/packages/hhsuite/trunk/debian/patches/ trunk/packages/hhsuite/trunk/debian/patches/Makefile trunk/packages/hhsuite/trunk/debian/patches/series trunk/packages/hhsuite/trunk/debian/rules trunk/packages/hhsuite/trunk/debian/source/ trunk/packages/hhsuite/trunk/debian/source/format trunk/packages/hhsuite/trunk/debian/watch Log: initial untested package of hhsuite that builds Property changes on: trunk/packages/hhsuite/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/hhsuite/trunk/debian/README.source =================================================================== --- trunk/packages/hhsuite/trunk/debian/README.source (rev 0) +++ trunk/packages/hhsuite/trunk/debian/README.source 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,10 @@ +hhsuite for Debian +------------------ + +Patches +....... + +patch1: +* ? + +# vim:et:ts=2: Added: trunk/packages/hhsuite/trunk/debian/changelog =================================================================== --- trunk/packages/hhsuite/trunk/debian/changelog (rev 0) +++ trunk/packages/hhsuite/trunk/debian/changelog 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,5 @@ +hhsuite (2.0.4-1) UNRELEASED; urgency=low + + * Initial release (Closes: #656626) + + -- Laszlo Kajan <[email protected]> Fri, 20 Jan 2012 15:10:40 +0100 Added: trunk/packages/hhsuite/trunk/debian/compat =================================================================== --- trunk/packages/hhsuite/trunk/debian/compat (rev 0) +++ trunk/packages/hhsuite/trunk/debian/compat 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +8 Added: trunk/packages/hhsuite/trunk/debian/control =================================================================== --- trunk/packages/hhsuite/trunk/debian/control (rev 0) +++ trunk/packages/hhsuite/trunk/debian/control 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,94 @@ +Source: hhsuite +Section: science +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Laszlo Kajan <[email protected]> +Build-Depends: debhelper (>= 8.0.0), libpng12-dev +Standards-Version: 3.9.2 +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 +Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex +Description: sensitive protein sequence searching based on HMM-HMM alignment + HH-suite is an open-source software package for sensitive protein sequence + searching based on the pairwise alignment of hidden Markov models (HMMs). + It contains HHsearch and HHblits among other programs and utilities. + . + HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM + and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous + proteins. HHsearch is often used for protein structure prediction to detect + homologous templates and to build highly accurate query-template pairwise + alignments for homology modeling. + . + HHblits can build high-quality MSAs starting from single sequences or from + MSAs. It transforms these into a query HMM and, using an iterative search + strategy, adds significantly similar sequences from the previous search to + the updated query HMM for the next search iteration. Compared to PSI-BLAST, + HHblits is faster, up to twice as sensitive and produces more accurate + alignments. + +Package: hhsuite-dbg +Architecture: amd64 +Section: debug +Priority: extra +Depends: hhsuite (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} +Description: sensitive protein sequence searching based on HMM-HMM alignment + This package contains the debugging symbols. + +Package: ffindex +Architecture: any +Depends: libffindex0 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} +Description: simple index/database for huge amounts of small files + FFindex is a very simple index/database for huge amounts of small files. The + files are stored concatenated in one big data file, separated by '\0'. A + second file contains a plain text index, giving name, offset and length of + the small files. The lookup is currently done with a binary search on an + array made from the index file. + . + This package provides the executables. + +Package: libffindex0 +Architecture: any +Section: libs +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: simple index/database for huge amounts of small files + FFindex is a very simple index/database for huge amounts of small files. The + files are stored concatenated in one big data file, separated by '\0'. A + second file contains a plain text index, giving name, offset and length of + the small files. The lookup is currently done with a binary search on an + array made from the index file. + . + This package provides the shared library. + +Package: libffindex0-dev +Architecture: any +Section: libdevel +Depends: libffindex0 (= ${binary:Version}), ${misc:Depends} +Provides: libffindex-dev +Description: simple index/database for huge amounts of small files + FFindex is a very simple index/database for huge amounts of small files. The + files are stored concatenated in one big data file, separated by '\0'. A + second file contains a plain text index, giving name, offset and length of + the small files. The lookup is currently done with a binary search on an + array made from the index file. + . + This package contains the header files and documentation + needed to develop applications with libffindex. + +Package: libffindex0-dbg +Architecture: any +Section: debug +Priority: extra +Depends: libffindex0 (= ${binary:Version}), ${misc:Depends} +Description: simple index/database for huge amounts of small files + FFindex is a very simple index/database for huge amounts of small files. The + files are stored concatenated in one big data file, separated by '\0'. A + second file contains a plain text index, giving name, offset and length of + the small files. The lookup is currently done with a binary search on an + array made from the index file. + . + This package provides the detached debug symbols for libffindex. Added: trunk/packages/hhsuite/trunk/debian/copyright =================================================================== --- trunk/packages/hhsuite/trunk/debian/copyright (rev 0) +++ trunk/packages/hhsuite/trunk/debian/copyright 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,47 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: hhsuite +Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/hhsuite-([0-9.]+)\.tar\.gz + +Files: src/fmemopen.c lib/ffindex/src/ext/fmemopen.c +Copyright: 2009 Open Information Security Foundation +License: GPL-2.0+ + +Files: src/cs/getopt_pp.h src/cs/getopt_pp.cc +Copyright: 2007, 2008 Daniel Gutson, FuDePAN +License: GPL-3.0+ + +Files: src/pngwriter.cc src/pngwriter.h +Copyright: 2002, 2003 Paul Blackburn +License: GPL + +Files: lib/ffindex/* +Copyright: Andy Hauser <[email protected]> +License: Create Commons license "Attribution-ShareAlike 3.0" + +Files: debian/* +Copyright: 2012 Laszlo Kajan <[email protected]> +License: GPL-3.0+ + +Files: * +Copyright: 2006, 2012 Johannes Soeding + 2012 Michael Remmert + 2012 Andreas Hauser <[email protected]> + 2006, 2009, 2012 Andreas Biegert +License: GPL-3.0+ + +License: GPL-3.0+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". Added: trunk/packages/hhsuite/trunk/debian/docs =================================================================== --- trunk/packages/hhsuite/trunk/debian/docs (rev 0) +++ trunk/packages/hhsuite/trunk/debian/docs 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +README Added: trunk/packages/hhsuite/trunk/debian/ffindex.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/ffindex.install (rev 0) +++ trunk/packages/hhsuite/trunk/debian/ffindex.install 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +usr/bin/ff* Added: trunk/packages/hhsuite/trunk/debian/hhsuite.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.install (rev 0) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.install 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,4 @@ +usr/bin/hh* +usr/lib/hhsuite/bin +usr/lib/hhsuite/data +usr/lib/hhsuite/scripts Added: trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install (rev 0) +++ trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,3 @@ +usr/include/* +usr/lib/libffindex.a +usr/lib/libffindex.so Added: trunk/packages/hhsuite/trunk/debian/libffindex0.install =================================================================== --- trunk/packages/hhsuite/trunk/debian/libffindex0.install (rev 0) +++ trunk/packages/hhsuite/trunk/debian/libffindex0.install 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +usr/lib/libffindex.so.* Added: trunk/packages/hhsuite/trunk/debian/patches/Makefile =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/Makefile (rev 0) +++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,252 @@ +Index: hhsuite-2.0.4/Makefile +=================================================================== +--- hhsuite-2.0.4.orig/Makefile 2012-01-20 20:17:19.000000000 +0100 ++++ hhsuite-2.0.4/Makefile 2012-01-20 20:18:42.504242187 +0100 +@@ -1,5 +1,5 @@ + # This can be overridden e.g.: make install INSTALL_DIR=... +-INSTALL_DIR?=$(PWD) ++INSTALL_DIR:=$(DESTDIR)/usr + + # Guess wether to use lib or lib64 + #libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib` +@@ -8,36 +8,38 @@ + + # Overriding this is currently not fully supported as the code won't know + # to what this is set then. You can try setting HHLIB. +-INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hh ++INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hhsuite + INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts + INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data + INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin + + dist_name=hhsuite-2.0.4 + +-all_static: ffindex_static +- cd src && make all_static +- ++.PHONY: all + all: ffindex +- cd src && make all ++ $(MAKE) -C src all ++ ++all_static: ffindex_static ++ $(MAKE) -C src all_static + + doc: +- cd src && make hhsuite-userguide.pdf ++ $(MAKE) -C src hhsuite-userguide.pdf + + hhblits_static: hhblits_static +- cd src && make hhblits_static ++ $(MAKE) -C src hhblits_static + + hhblits: ffindex +- cd src && make all ++ $(MAKE) -C src all + ++.PHONY: ffindex + ffindex: +- cd lib/ffindex && make ++ $(MAKE) -C lib/ffindex + + ffindex_static: +- cd lib/ffindex && make FFINDEX_STATIC=1 ++ $(MAKE) -C lib/ffindex FFINDEX_STATIC=1 + + install: +- cd lib/ffindex && make install INSTALL_DIR=$(INSTALL_DIR) ++ $(MAKE) -C lib/ffindex install INSTALL_DIR=$(INSTALL_DIR) + mkdir -p $(INSTALL_DIR)/bin + install src/hhblits $(INSTALL_DIR)/bin/hhblits + install src/hhalign $(INSTALL_DIR)/bin/hhalign +@@ -49,23 +51,23 @@ + mkdir -p $(INSTALL_LIB_BIN_DIR) + install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate + mkdir -p $(INSTALL_DATA_DIR) +- install data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib +- install data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib +- install data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete +- install data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr +- install data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin +- install data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq ++ install --mode=0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib ++ install --mode=0644 data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib ++ install --mode=0644 data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete ++ install --mode=0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr ++ install --mode=0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin ++ install --mode=0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq + mkdir -p $(INSTALL_SCRIPTS_DIR) +- install scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm +- install scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm ++ install --mode=0644 scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm ++ install --mode=0644 scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm + install scripts/addss.pl $(INSTALL_SCRIPTS_DIR)/addss.pl + install scripts/create_profile_from_hhm.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl + install scripts/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl + install scripts/hhmakemodel.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl + install scripts/reformat.pl $(INSTALL_SCRIPTS_DIR)/reformat.pl + +-deinstall: +- cd lib/ffindex && make deinstall INSTALL_DIR=$(INSTALL_DIR) ++uninstall: ++ $(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR) + rm -f $(INSTALL_DIR)/bin/hhblits $(INSTALL_DIR)/bin/hhalign \ + $(INSTALL_DIR)/bin/hhconsensus $(INSTALL_DIR)/bin/hhfilter $(INSTALL_DIR)/bin/hhmake $(INSTALL_DIR)/bin/hhsearch + rm -f $(INSTALL_DATA_DIR)/context_data.lib $(INSTALL_DATA_DIR)/cs219.lib $(INSTALL_DATA_DIR)/do_not_delete \ +@@ -81,9 +83,10 @@ + rmdir $(INSTALL_SCRIPTS_DIR) || true + rmdir $(INSTALL_LIB_DIR) || true + ++.PHONY: clean + clean: +- cd lib/ffindex && make clean +- cd src && make clean ++ $(MAKE) -C lib/ffindex clean ++ $(MAKE) -C src clean + + dist/$(dist_name).tar.gz: + make clean +Index: hhsuite-2.0.4/scripts/HHPaths.pm +=================================================================== +--- hhsuite-2.0.4.orig/scripts/HHPaths.pm 2012-01-20 20:17:19.000000000 +0100 ++++ hhsuite-2.0.4/scripts/HHPaths.pm 2012-01-20 20:18:42.512254195 +0100 +@@ -39,7 +39,7 @@ + # The lines below probably do not need to be changed + + # Setting paths for hh-suite perl scripts +-our $hhlib = $ENV{"HHLIB"}; # main hh-suite directory ++our $hhlib = "/usr/lib/hhsuite"; # main hh-suite directory + our $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files + our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in $PATH) + our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.) +Index: hhsuite-2.0.4/src/hhdecl.C +=================================================================== +--- hhsuite-2.0.4.orig/src/hhdecl.C 2012-01-20 20:17:19.000000000 +0100 ++++ hhsuite-2.0.4/src/hhdecl.C 2012-01-20 20:18:42.528243118 +0100 +@@ -286,10 +286,10 @@ + { + // set hhlib + FILE* testf = NULL; +- if(getenv("HHLIB")) +- strcpy(hhlib, getenv("HHLIB")); +- else +- strcpy(hhlib, "/usr/lib/hh"); ++// if(getenv("HHLIB")) ++// strcpy(hhlib, getenv("HHLIB")); ++// else ++ strcpy(hhlib, "/usr/lib/hhsuite"); + + strcat(strcpy(hhdata, hhlib), "/data"); + strcat(strcpy(clusterfile, hhdata), "/context_data.lib"); +@@ -301,7 +301,7 @@ + /* we did not find HHLIB, if called with full path or in dist dir, we can try relative to program path */ + if(program_path != NULL) + { +- strcat(strcpy(hhlib, program_path), "../lib/hh"); ++ strcat(strcpy(hhlib, program_path), "../lib/hhsuite"); + strcat(strcpy(hhdata, hhlib), "/data"); + strcat(strcpy(clusterfile, hhdata), "/context_data.lib"); + strcat(strcpy(cs_library, hhdata), "/cs219.lib"); +Index: hhsuite-2.0.4/lib/ffindex/Makefile +=================================================================== +--- hhsuite-2.0.4.orig/lib/ffindex/Makefile 2012-01-20 20:17:19.000000000 +0100 ++++ hhsuite-2.0.4/lib/ffindex/Makefile 2012-01-20 20:18:42.540241867 +0100 +@@ -7,13 +7,7 @@ + endif + + all: +- cd src ; make -f $(MFILE) ++ $(MAKE) -C src $@ + +-install: +- cd src ; make install +- +-deinstall: +- cd src ; make deinstall +- +-clean: +- cd src ; make clean ++%: ++ $(MAKE) -C src $@ +Index: hhsuite-2.0.4/lib/ffindex/src/Makefile +=================================================================== +--- hhsuite-2.0.4.orig/lib/ffindex/src/Makefile 2012-01-20 20:17:19.000000000 +0100 ++++ hhsuite-2.0.4/lib/ffindex/src/Makefile 2012-01-20 21:33:12.932241991 +0100 +@@ -1,12 +1,14 @@ + INSTALL_DIR?=.. +-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib` ++libdir=lib + LANG=C + CFLAGS+=-std=c99 -openmp -g -fPIC -Wall ++SOCURRENT=0 ++SOVERSION=$(SOCURRENT).1.0 + ifdef FFINDEX_STATIC + LDFLAGS+=-static + FFINDEX_OBJECTS=libffindex.a + else +- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1 ++ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION) + endif + + #-Wl,--version-script=libffindex.map +@@ -24,11 +26,12 @@ + ffindex_modify: $(FFINDEX_OBJECTS) ffindex_modify.o ffindex.h + $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex + +-libffindex.so.0.1: ffindex.o ffutil.o +- $(CC) -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o libffindex.so.0.1 ffindex.o ffutil.o -lc ++libffindex.so.$(SOVERSION): ffindex.o ffutil.o ++ $(CC) -Wl,-z,defs,-z,noexecstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc + +-libffindex.so: libffindex.so.0.1 +- ln -sf libffindex.so.0.1 libffindex.so ++libffindex.so: libffindex.so.$(SOVERSION) ++ ln -sf libffindex.so.$(SOVERSION) libffindex.so.$(SOCURRENT) ++ ln -sf libffindex.so.$(SOVERSION) libffindex.so + + libffindex.a: ffindex.o ffutil.o + ar rcs libffindex.a ffutil.o ffindex.o +@@ -53,7 +56,7 @@ + LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" zsh -c "time ./ffindex_get ../test_big/nr20_11Jan10_a3m_db ../test_big/nr20_11Jan10_a3m_db.ffindex BABBAMIBA.a3m KARDUZEBA.a3m HARPAQIBA.a3m WOQQATEBA.a3m BEBRAQIBA.a3m GIRSAKEBA.a3m NAQTIFIBA.a3m BIWCIQABA.a3m > /dev/null" + + clean: +- rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 ffindex_modify ffindex_modify.o libffindex.a ++ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOCURRENT) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o libffindex.a + + install: + mkdir -p $(INSTALL_DIR)/bin +@@ -62,16 +65,17 @@ + install ffindex_get $(INSTALL_DIR)/bin/ffindex_get + install ffindex_build $(INSTALL_DIR)/bin/ffindex_build + install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify +- install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 ++ install libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION) + install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a +- ln -sf libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so ++ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT) ++ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so + install ffindex.h $(INSTALL_DIR)/include/ffindex.h + install ffutil.h $(INSTALL_DIR)/include/ffutil.h + + deinstall: + rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \ +- $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.a \ +- $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h ++ $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.a \ ++ $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT) $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h + rmdir $(INSTALL_DIR)/bin || true + rmdir $(INSTALL_DIR)/$(libdir) || true + rmdir $(INSTALL_DIR)/include || true +Index: hhsuite-2.0.4/src/Makefile +=================================================================== +--- hhsuite-2.0.4.orig/src/Makefile 2012-01-20 20:43:18.024242503 +0100 ++++ hhsuite-2.0.4/src/Makefile 2012-01-20 20:43:41.984242663 +0100 +@@ -31,7 +31,7 @@ + ifeq ($(OS), Linux) + HHSEARCH_LIBS = -lpthread -lrt + HHLIBS+=-lrt +- HHALIGN_LIBS = -DHH_PNG -lpng -lz -I/usr/include/ -L/usr/lib ++ HHALIGN_LIBS = -DHH_PNG -lpng -I/usr/include/ -L/usr/lib + endif + endif + Added: trunk/packages/hhsuite/trunk/debian/patches/series =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/series (rev 0) +++ trunk/packages/hhsuite/trunk/debian/patches/series 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +Makefile Added: trunk/packages/hhsuite/trunk/debian/rules =================================================================== --- trunk/packages/hhsuite/trunk/debian/rules (rev 0) +++ trunk/packages/hhsuite/trunk/debian/rules 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,18 @@ +#!/usr/bin/make -f + +# Uncomment this to turn on verbose mode. +export DH_VERBOSE=1 + +%: + dh $@ + +.PHONY: override_dh_auto_build +override_dh_auto_build: + # parallel build: e.g. for -j12 we get parallel=12 in DEB_BUILD_OPTIONS, the -j12 on dpkg-buildpackage does not seem to be passed down in any other way + #echo '$(MAKE)' '$(MAKEFLAGS)' '$(DEB_BUILD_OPTIONS)' + parallel=1 && eval $(DEB_BUILD_OPTIONS) && make -j$$parallel + +.PHONY: override_dh_strip +override_dh_strip: + dh_strip --dbg-package=libffindex0-dbg -Xffindex_build -Xffindex_get -Xffindex_modify -Xhhalign -Xhhblits -Xhhconsensus -Xhhfilter -Xhhmake -Xhhsearch -Xcstranslate + dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so Property changes on: trunk/packages/hhsuite/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/hhsuite/trunk/debian/source/format =================================================================== --- trunk/packages/hhsuite/trunk/debian/source/format (rev 0) +++ trunk/packages/hhsuite/trunk/debian/source/format 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/hhsuite/trunk/debian/watch =================================================================== --- trunk/packages/hhsuite/trunk/debian/watch (rev 0) +++ trunk/packages/hhsuite/trunk/debian/watch 2012-01-20 21:02:42 UTC (rev 9354) @@ -0,0 +1,3 @@ +version=3 + +ftp://toolkit.lmb.uni-muenchen.de/HH-suite/hhsuite-([0-9.]+)\.tar\.gz debian uupdate _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
