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 <[email protected]>] + debian/upstream: Enhanced author values + * [Laszlo Kajan <[email protected]>] + New upstream release. - -- Andreas Tille <[email protected]> Mon, 07 May 2012 23:12:02 +0200 + -- Laszlo Kajan <[email protected]> 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 $(MAKE) -C for making in subdirectories -* fix install mode of data files -* deinstall -> uninstall -* fix issues where the path in help pages is taken from the build-time location of the executables +Description: Patch to top level Makefile + * Make Makefile DESTDIR-aware. + * Fix install mode of data files. +Forwarded: upstream is aware of these patches + Upstream is Andreas Hauser <[email protected]>. +Author: Laszlo Kajan <[email protected]> --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ @@ -26,7 +27,7 @@ +INSTALL_BDATA_DIR?=$(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 [email protected] - --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 [email protected] - --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 [email protected] - --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 [email protected] - --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 [email protected] - --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 [email protected] - --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 [email protected] - --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 <[email protected]> +--- 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 <[email protected]> +--- 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 <[email protected]> +--- 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 [email protected] + +-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 [email protected] + +-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 [email protected] + +-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 [email protected] + +-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 [email protected] + +-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 [email protected] + +-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 [email protected] + +-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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
