[med-svn] r10958 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed May 23 12:16:49 UTC 2012
Author: lkajan-guest
Date: 2012-05-23 12:16:48 +0000 (Wed, 23 May 2012)
New Revision: 10958
Added:
trunk/packages/hhsuite/trunk/debian/patches/help
trunk/packages/hhsuite/trunk/debian/patches/paths
trunk/packages/hhsuite/trunk/debian/patches/rest1
Modified:
trunk/packages/hhsuite/trunk/debian/changelog
trunk/packages/hhsuite/trunk/debian/patches/Makefile
trunk/packages/hhsuite/trunk/debian/patches/series
Log:
patches updated for version 2.0.14
Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog 2012-05-23 04:32:33 UTC (rev 10957)
+++ trunk/packages/hhsuite/trunk/debian/changelog 2012-05-23 12:16:48 UTC (rev 10958)
@@ -1,8 +1,11 @@
-hhsuite (2.0.13-3) UNRELEASED; urgency=low
+hhsuite (2.0.14-1) UNRELEASED; urgency=low
- * debian/upstream: Enhanced author values
+ * [Andreas Tille <tille at debian.org>]
+ debian/upstream: Enhanced author values
+ * [Laszlo Kajan <lkajan at rostlab.org>]
+ New upstream release.
- -- Andreas Tille <tille at debian.org> Mon, 07 May 2012 23:12:02 +0200
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 23 May 2012 10:52:40 +0200
hhsuite (2.0.13-2) unstable; urgency=low
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-05-23 04:32:33 UTC (rev 10957)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-05-23 12:16:48 UTC (rev 10958)
@@ -1,8 +1,9 @@
-* make Makefile DESTDIR-aware
-* use $(MAKE) -C for making in subdirectories
-* fix install mode of data files
-* deinstall -> uninstall
-* fix issues where the path in help pages is taken from the build-time location of the executables
+Description: Patch to top level Makefile
+ * Make Makefile DESTDIR-aware.
+ * Fix install mode of data files.
+Forwarded: upstream is aware of these patches
+ Upstream is Andreas Hauser <hauser at genzentrum.lmu.de>.
+Author: Laszlo Kajan <lkajan at rostlab.org>
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
@@ -26,7 +27,7 @@
+INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data
INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
- dist_name=hhsuite-2.0.13
+ dist_name=hhsuite-2.0.14
-.PHONY: all_static
-all_static: ffindex_static
@@ -116,216 +117,3 @@
dist/$(dist_name).tar.gz:
make clean
mkdir -p dist
---- a/scripts/HHPaths.pm
-+++ b/scripts/HHPaths.pm
-@@ -14,7 +14,7 @@
- use Exporter;
- our $VERSION = "version 2.0.12 (Feb 2012)";
- our @ISA = qw(Exporter);
--our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
-+our @EXPORT = qw($VERSION $hhlib $hhshare $hhdata $hhbdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
-
- ##############################################################################################
- # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED)
-@@ -38,11 +38,13 @@
- # 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 $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files
-+our $hhlib = $ENV{"HHLIB"} || "/usr/lib/hhsuite"; # main hh-suite directory
-+our $hhshare = $ENV{"HHLIB"} || "/usr/share/hhsuite"; # main hh-suite directory
-+our $hhdata = $hhshare."/data"; # path to arch indep data directory for hhblits, example files
-+our $hhbdata = $hhlib."/data"; # path to arch dep 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.)
--our $dummydb = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
-+our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
-+our $dummydb = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
-
- # HHblits data files
- our $cs_lib = "$hhdata/cs219.lib";
---- a/src/hhdecl.C
-+++ b/src/hhdecl.C
-@@ -279,7 +279,7 @@
- if(getenv("HHLIB"))
- strcpy(hhlib, getenv("HHLIB"));
- else
-- strcpy(hhlib, "/usr/lib/hh");
-+ strcpy(hhlib, "/usr/lib/hhsuite");
-
- strcat(strcpy(hhdata, hhlib), "/data");
- strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
-@@ -291,7 +291,7 @@
- /* 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");
---- a/src/hhblits.C
-+++ b/src/hhblits.C
-@@ -295,8 +295,8 @@
- printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
- if (all) {
- printf("Directory paths \n");
-- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile);
-- printf(" -cslib <file> column state file for fast database prefiltering (default=%s)\n",par.cs_library);
-+ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n");
-+ printf(" -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n");
- printf(" -psipred <dir> directory with PSIPRED executables (default=%s) \n",par.psipred);
- printf(" -psipred_data <dir> directory with PSIPRED data (default=%s) \n",par.psipred_data);
- printf("\n");
-@@ -408,7 +408,12 @@
- printf("An extended list of options can be obtained by using '-help all' as parameter \n");
- }
- printf("\n");
-- printf("Example: %s -i query.fas -oa3m query.a3m -n 2 \n",program_name);
-+ printf("Examples:\n");
-+ printf("%s -i query.fas -o query.hhr -d <database-basepath>\n",program_name);
-+ printf("\n");
-+ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 2 -d <database-basepath>\n",program_name);
-+ printf("\n");
-+ printf("Download databases from ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/hhblits/.\n");
- cout<<endl;
- }
-
---- a/src/hhsearch.C
-+++ b/src/hhsearch.C
-@@ -40,6 +40,7 @@
- #include <float.h> // FLT_MIN
- #include <ctype.h> // islower, isdigit etc
- #include <time.h> // clock_gettime etc. (in realtime library (-lrt compiler option))
-+#include <unistd.h>
- #include <errno.h> // perror()
- #include <cassert>
- #include <stdexcept>
-@@ -326,7 +327,7 @@
- printf(" -pcc [0,3] extinction exponent for tau(Neff) (def=%-.1f) \n",par.pcc);
- printf(" -pcw [0,3] weight of pos-specificity for pcs (def=%-.1f) \n",par.pcw);
- // HHsearch option should be the same as HHblits option!!
-- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile);
-+ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n");
- printf(" -csw [0,inf] weight of central position in cs pseudocount mode (def=%.1f)\n", par.csw);
- printf(" -csb [0,1] weight decay parameter for positions in cs pc mode (def=%.1f)\n", par.csb);
- }
---- a/src/Makefile
-+++ b/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$(CS_DIR)
- HHSEARCH_LIBS = -lpthread -lrt
- HHBLITS_LIBS = -lpthread -lrt -openmp
- OBJECT_LIBS = -openmp
- else # ifndef ICC
- CXX = g++
-- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR)
-+ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG)
- HHSEARCH_LIBS = -lpthread
- HHBLITS_LIBS = -lpthread -fopenmp
- HHALIGN_LIBS =
-@@ -92,7 +92,7 @@
- $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
-
- hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
-- $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
-+ $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex
-
- hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
- $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
---- a/scripts/addss.pl
-+++ b/scripts/addss.pl
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use Align; # Needleman-Wunsch and Smith-Waterman alignment functions
- use File::Temp qw/ tempfile tempdir /;
---- a/scripts/hhblitsdb.pl
-+++ b/scripts/hhblitsdb.pl
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
-
---- a/scripts/hhmakemodel.pl
-+++ b/scripts/hhmakemodel.pl
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
- use Align;
---- /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
---- a/scripts/create_profile_from_hhm.pl
-+++ b/scripts/create_profile_from_hhm.pl
-@@ -27,7 +27,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
-
---- a/scripts/create_profile_from_hmmer.pl
-+++ b/scripts/create_profile_from_hmmer.pl
-@@ -27,7 +27,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
-
---- a/scripts/multithread.pl
-+++ b/scripts/multithread.pl
-@@ -29,7 +29,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
- use POSIX;
---- a/scripts/reformat.pl
-+++ b/scripts/reformat.pl
-@@ -27,7 +27,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
- use warnings;
Added: trunk/packages/hhsuite/trunk/debian/patches/help
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/help (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/help 2012-05-23 12:16:48 UTC (rev 10958)
@@ -0,0 +1,52 @@
+Description: fix paths in help pages
+ Fix issues where the path in help pages is taken from the build-time location of the executables.
+Forwarded: not-needed
+Author: Laszlo Kajan <lkajan at rostlab.org>
+--- a/src/hhblits.C
++++ b/src/hhblits.C
+@@ -382,8 +382,8 @@
+ printf("\n");
+ printf("Context-specific pseudo-counts: \n");
+ printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n");
+- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile);
+- printf(" -cslib <file> column state file for fast database prefiltering (default=%s)\n",par.cs_library);
++ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n");
++ printf(" -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n");
+ printf("\n");
+ printf("Predict secondary structure\n");
+ printf(" -addss add 2ndary structure predicted with PSIPRED to output MSA \n");
+@@ -412,7 +412,12 @@
+ printf("An extended list of options can be obtained by calling 'hhblits -help'\n");
+ }
+ printf("\n");
+- printf("Example: %s -i query.fas -oa3m query.a3m -n 1 \n",program_name);
++ printf("Examples:\n");
++ printf("%s -i query.fas -o query.hhr -d <database-basepath>\n",program_name);
++ printf("\n");
++ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d <database-basepath>\n",program_name);
++ printf("\n");
++ printf("Download databases from ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/ .\n");
+ cout<<endl;
+ }
+
+--- a/src/hhsearch.C
++++ b/src/hhsearch.C
+@@ -41,6 +41,7 @@
+ #include <float.h> // FLT_MIN
+ #include <ctype.h> // islower, isdigit etc
+ #include <time.h> // clock_gettime etc. (in realtime library (-lrt compiler option))
++#include <unistd.h>
+ #include <errno.h> // perror()
+ #include <cassert>
+ #include <stdexcept>
+@@ -301,8 +302,8 @@
+ printf("\n");
+ printf("Context-specific pseudo-counts: \n");
+ printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n");
+- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile);
+- printf(" -cslib <file> column state file for fast database prefiltering (default=%s)\n",par.cs_library);
++ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n");
++ printf(" -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n");
+ if (all) {
+ printf(" -csw [0,inf] weight of central position in cs pseudocount mode (def=%.1f)\n", par.csw);
+ printf(" -csb [0,1] weight decay parameter for positions in cs pc mode (def=%.1f)\n", par.csb);
Added: trunk/packages/hhsuite/trunk/debian/patches/paths
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/paths (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/paths 2012-05-23 12:16:48 UTC (rev 10958)
@@ -0,0 +1,53 @@
+Description: Set hhsuite paths.
+ Set paths to hhsuite components - as installed on Debian - correctly in absence of the (now superflouos) HHLIB environment variable.
+Forwarded: not-needed
+Author: Laszlo Kajan <lkajan at rostlab.org>
+--- a/scripts/HHPaths.pm
++++ b/scripts/HHPaths.pm
+@@ -30,7 +30,7 @@
+ use Exporter;
+ our $VERSION = "version 2.0.14 (Mar 2012)";
+ our @ISA = qw(Exporter);
+-our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
++our @EXPORT = qw($VERSION $hhlib $hhshare $hhdata $hhbdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
+
+ ##############################################################################################
+ # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED)
+@@ -54,11 +54,13 @@
+ # 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 $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files
++our $hhlib = $ENV{"HHLIB"} || "/usr/lib/hhsuite"; # main hh-suite directory
++our $hhshare = $ENV{"HHLIB"} || "/usr/share/hhsuite"; # main hh-suite directory
++our $hhdata = $hhshare."/data"; # path to arch indep data directory for hhblits, example files
++our $hhbdata = $hhlib."/data"; # path to arch dep data directory for hhblits, example files
+ our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH)
+-our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
+-our $dummydb = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
++our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
++our $dummydb = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
+
+ # HHblits data files
+ our $cs_lib = "$hhdata/cs219.lib";
+--- a/src/hhdecl.C
++++ b/src/hhdecl.C
+@@ -280,7 +280,7 @@
+ if(getenv("HHLIB"))
+ strcpy(hhlib, getenv("HHLIB"));
+ else
+- strcpy(hhlib, "/usr/lib/hh");
++ strcpy(hhlib, "/usr/lib/hhsuite");
+
+ strcat(strcpy(hhdata, hhlib), "/data");
+ strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
+@@ -295,7 +295,7 @@
+ /* 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");
Added: trunk/packages/hhsuite/trunk/debian/patches/rest1
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/rest1 (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/rest1 2012-05-23 12:16:48 UTC (rev 10958)
@@ -0,0 +1,122 @@
+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 <lkajan at rostlab.org>
+--- a/src/Makefile
++++ b/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$(CS_DIR)
+ HHSEARCH_LIBS = -lpthread -lrt
+ HHBLITS_LIBS = -lpthread -lrt -openmp
+ OBJECT_LIBS = -openmp
+ else # ifndef ICC
+ CXX = g++
+- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR)
++ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG)
+ HHSEARCH_LIBS = -lpthread
+ HHBLITS_LIBS = -lpthread -fopenmp
+ HHALIGN_LIBS =
+@@ -92,7 +92,7 @@
+ $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
+
+ hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
+- $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
++ $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex
+
+ hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
+ $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
+--- a/scripts/addss.pl
++++ b/scripts/addss.pl
+@@ -28,7 +28,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use Align; # Needleman-Wunsch and Smith-Waterman alignment functions
+ use File::Temp qw/ tempfile tempdir /;
+--- a/scripts/hhblitsdb.pl
++++ b/scripts/hhblitsdb.pl
+@@ -28,7 +28,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+--- a/scripts/hhmakemodel.pl
++++ b/scripts/hhmakemodel.pl
+@@ -28,7 +28,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use Align;
+--- /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
+--- a/scripts/create_profile_from_hhm.pl
++++ b/scripts/create_profile_from_hhm.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+--- a/scripts/create_profile_from_hmmer.pl
++++ b/scripts/create_profile_from_hmmer.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+--- a/scripts/multithread.pl
++++ b/scripts/multithread.pl
+@@ -29,7 +29,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use POSIX;
+--- a/scripts/reformat.pl
++++ b/scripts/reformat.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use warnings;
Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series 2012-05-23 04:32:33 UTC (rev 10957)
+++ trunk/packages/hhsuite/trunk/debian/patches/series 2012-05-23 12:16:48 UTC (rev 10958)
@@ -1 +1,4 @@
Makefile
+paths
+help
+rest1
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