[med-svn] r9354 - in trunk/packages/hhsuite: . trunk trunk/debian trunk/debian/patches trunk/debian/source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Fri Jan 20 21:02:42 UTC 2012
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 <lkajan at rostlab.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+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 <hauser at genzentrum.lmu.de>
+License: Create Commons license "Attribution-ShareAlike 3.0"
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-3.0+
+
+Files: *
+Copyright: 2006, 2012 Johannes Soeding
+ 2012 Michael Remmert
+ 2012 Andreas Hauser <hauser at genzentrum.lmu.de>
+ 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
More information about the debian-med-commit
mailing list