Author: lkajan-guest Date: 2012-02-22 11:20:09 +0000 (Wed, 22 Feb 2012) New Revision: 9750
Added: trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base Modified: trunk/packages/hhsuite/trunk/debian/changelog trunk/packages/hhsuite/trunk/debian/control trunk/packages/hhsuite/trunk/debian/patches/Makefile trunk/packages/hhsuite/trunk/debian/patches/default_path trunk/packages/hhsuite/trunk/debian/rules trunk/packages/hhsuite/trunk/debian/upstream trunk/packages/hhsuite/trunk/debian/watch Log: upgrade to upstream version 2.0.12 Modified: trunk/packages/hhsuite/trunk/debian/changelog =================================================================== --- trunk/packages/hhsuite/trunk/debian/changelog 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/changelog 2012-02-22 11:20:09 UTC (rev 9750) @@ -1,5 +1,5 @@ -hhsuite (2.0.5-1) UNRELEASED; urgency=low +hhsuite (2.0.12-1) UNRELEASED; urgency=low * Initial release (Closes: #656626) - -- Laszlo Kajan <[email protected]> Fri, 20 Jan 2012 15:10:40 +0100 + -- Laszlo Kajan <[email protected]> Wed, 22 Feb 2012 10:03:00 +0100 Modified: trunk/packages/hhsuite/trunk/debian/control =================================================================== --- trunk/packages/hhsuite/trunk/debian/control 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/control 2012-02-22 11:20:09 UTC (rev 9750) @@ -16,8 +16,9 @@ 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. . + This package 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 @@ -37,6 +38,9 @@ Priority: extra Depends: hhsuite (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} Description: sensitive protein sequence searching based on HMM-HMM alignment + HH-suite is an open-source software package for sensitive protein sequence + searching based on the pairwise alignment of hidden Markov models (HMMs). + . This package contains the debugging symbols. Package: ffindex Added: trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base =================================================================== --- trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base (rev 0) +++ trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base 2012-02-22 11:20:09 UTC (rev 9750) @@ -0,0 +1,8 @@ +Document: hhsuite +Title: HH-suite User Guide +Author: Johannes Söding, Michael Remmert, Andreas Hauser +Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-02-22 11:20:09 UTC (rev 9750) @@ -1,7 +1,7 @@ -Index: hhsuite-2.0.5/Makefile +Index: hhsuite-2.0.12/Makefile =================================================================== ---- hhsuite-2.0.5.orig/Makefile 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/Makefile 2012-01-24 18:05:59.980241952 +0100 +--- hhsuite-2.0.12.orig/Makefile 2012-02-17 13:52:02.000000000 +0100 ++++ hhsuite-2.0.12/Makefile 2012-02-22 10:19:29.386857448 +0100 @@ -1,5 +1,5 @@ # This can be overridden e.g.: make install INSTALL_DIR=... -INSTALL_DIR?=$(PWD) @@ -19,7 +19,7 @@ INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin - dist_name=hhsuite-2.0.5 + dist_name=hhsuite-2.0.12 -all_static: ffindex_static - cd src && make all_static @@ -59,7 +59,7 @@ mkdir -p $(INSTALL_DIR)/bin install src/hhblits $(INSTALL_DIR)/bin/hhblits install src/hhalign $(INSTALL_DIR)/bin/hhalign -@@ -49,23 +51,23 @@ +@@ -49,15 +51,15 @@ mkdir -p $(INSTALL_LIB_BIN_DIR) install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate mkdir -p $(INSTALL_DATA_DIR) @@ -83,8 +83,9 @@ 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 +@@ -66,8 +68,8 @@ + install scripts/multithread.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl + install scripts/hhblitsdb.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl -deinstall: - cd lib/ffindex && make deinstall INSTALL_DIR=$(INSTALL_DIR) @@ -93,7 +94,7 @@ 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 @@ +@@ -83,9 +85,10 @@ rmdir $(INSTALL_SCRIPTS_DIR) || true rmdir $(INSTALL_LIB_DIR) || true @@ -106,11 +107,11 @@ dist/$(dist_name).tar.gz: make clean -Index: hhsuite-2.0.5/scripts/HHPaths.pm +Index: hhsuite-2.0.12/scripts/HHPaths.pm =================================================================== ---- hhsuite-2.0.5.orig/scripts/HHPaths.pm 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/scripts/HHPaths.pm 2012-01-24 17:57:52.632242731 +0100 -@@ -39,7 +39,7 @@ +--- hhsuite-2.0.12.orig/scripts/HHPaths.pm 2012-02-17 13:52:02.000000000 +0100 ++++ hhsuite-2.0.12/scripts/HHPaths.pm 2012-02-22 10:09:29.891044474 +0100 +@@ -38,7 +38,7 @@ # The lines below probably do not need to be changed # Setting paths for hh-suite perl scripts @@ -119,11 +120,11 @@ 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-2.0.5/src/hhdecl.C +Index: hhsuite-2.0.12/src/hhdecl.C =================================================================== ---- hhsuite-2.0.5.orig/src/hhdecl.C 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/src/hhdecl.C 2012-01-24 17:57:52.644242147 +0100 -@@ -289,7 +289,7 @@ +--- hhsuite-2.0.12.orig/src/hhdecl.C 2012-02-17 13:52:02.000000000 +0100 ++++ hhsuite-2.0.12/src/hhdecl.C 2012-02-22 10:24:33.614919605 +0100 +@@ -278,7 +278,7 @@ if(getenv("HHLIB")) strcpy(hhlib, getenv("HHLIB")); else @@ -132,7 +133,7 @@ strcat(strcpy(hhdata, hhlib), "/data"); strcat(strcpy(clusterfile, hhdata), "/context_data.lib"); -@@ -301,7 +301,7 @@ +@@ -290,7 +290,7 @@ /* 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) { @@ -141,19 +142,19 @@ strcat(strcpy(hhdata, hhlib), "/data"); strcat(strcpy(clusterfile, hhdata), "/context_data.lib"); strcat(strcpy(cs_library, hhdata), "/cs219.lib"); -@@ -316,7 +316,7 @@ +@@ -305,7 +305,7 @@ if (testf) { fclose(testf); return;} } -- cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib.\nPlease set the HHLIB environment variable to the HH-suite directory (under Linux: export HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n "; -+ cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib in '" << hhlib << "'.\nPlease set the HHLIB environment variable to the HH-suite directory (under Linux: export HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n "; +- cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib.\nPlease set the HHLIB environment variable to the HH-suite directory (Linux bash: export HHLIB=<hh_dir>, csh/tcsh: setenv HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n "; ++ cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib in '" << hhlib << "'.\nPlease set the HHLIB environment variable to the HH-suite directory (Linux bash: export HHLIB=<hh_dir>, csh/tcsh: setenv HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n "; exit(2); } -Index: hhsuite-2.0.5/lib/ffindex/Makefile +Index: hhsuite-2.0.12/lib/ffindex/Makefile =================================================================== ---- hhsuite-2.0.5.orig/lib/ffindex/Makefile 2012-01-19 14:06:31.000000000 +0100 -+++ hhsuite-2.0.5/lib/ffindex/Makefile 2012-01-24 17:57:52.652243178 +0100 +--- hhsuite-2.0.12.orig/lib/ffindex/Makefile 2012-01-19 14:06:31.000000000 +0100 ++++ hhsuite-2.0.12/lib/ffindex/Makefile 2012-02-22 10:09:29.907007650 +0100 @@ -7,13 +7,7 @@ endif @@ -171,10 +172,10 @@ - cd src ; make clean +%: + $(MAKE) -C src $@ -Index: hhsuite-2.0.5/lib/ffindex/src/Makefile +Index: hhsuite-2.0.12/lib/ffindex/src/Makefile =================================================================== ---- hhsuite-2.0.5.orig/lib/ffindex/src/Makefile 2012-01-19 14:06:31.000000000 +0100 -+++ hhsuite-2.0.5/lib/ffindex/src/Makefile 2012-01-24 17:57:52.656243179 +0100 +--- hhsuite-2.0.12.orig/lib/ffindex/src/Makefile 2012-01-19 14:06:31.000000000 +0100 ++++ hhsuite-2.0.12/lib/ffindex/src/Makefile 2012-02-22 10:09:29.919044543 +0100 @@ -1,12 +1,14 @@ INSTALL_DIR?=.. -libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib` @@ -240,16 +241,16 @@ rmdir $(INSTALL_DIR)/bin || true rmdir $(INSTALL_DIR)/$(libdir) || true rmdir $(INSTALL_DIR)/include || true -Index: hhsuite-2.0.5/src/Makefile +Index: hhsuite-2.0.12/src/Makefile =================================================================== ---- hhsuite-2.0.5.orig/src/Makefile 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/src/Makefile 2012-01-24 17:57:52.660242672 +0100 -@@ -31,7 +31,7 @@ - ifeq ($(OS), Linux) +--- hhsuite-2.0.12.orig/src/Makefile 2012-02-17 13:52:02.000000000 +0100 ++++ hhsuite-2.0.12/src/Makefile 2012-02-22 10:24:47.806919585 +0100 +@@ -46,7 +46,7 @@ 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 - + HHBLITS_LIBS+=-lrt + ifndef NO_PNG +- HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng -lz ++ HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng + endif + endif + endif # ifndef ICC Modified: trunk/packages/hhsuite/trunk/debian/patches/default_path =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-02-22 11:20:09 UTC (rev 9750) @@ -1,7 +1,7 @@ -Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_build.c +Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c =================================================================== ---- hhsuite-2.0.5.orig/lib/ffindex/src/ffindex_build.c 2012-01-19 14:06:31.000000000 +0100 -+++ hhsuite-2.0.5/lib/ffindex/src/ffindex_build.c 2012-01-24 18:13:02.000000000 +0100 +--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_build.c 2012-02-22 10:33:59.075044452 +0100 ++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c 2012-02-22 10:34:01.415044434 +0100 @@ -31,7 +31,7 @@ void usage(char *program_name) @@ -20,10 +20,10 @@ } int main(int argn, char **argv) -Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_get.c +Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c =================================================================== ---- hhsuite-2.0.5.orig/lib/ffindex/src/ffindex_get.c 2012-01-19 14:06:31.000000000 +0100 -+++ hhsuite-2.0.5/lib/ffindex/src/ffindex_get.c 2012-01-24 18:13:02.000000000 +0100 +--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_get.c 2012-02-22 10:33:59.099044560 +0100 ++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c 2012-02-22 10:34:01.419044624 +0100 @@ -26,9 +26,8 @@ { if(argn < 3) @@ -36,10 +36,10 @@ return -1; } char *data_filename = argv[1]; -Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_modify.c +Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c =================================================================== ---- hhsuite-2.0.5.orig/lib/ffindex/src/ffindex_modify.c 2012-01-19 14:06:31.000000000 +0100 -+++ hhsuite-2.0.5/lib/ffindex/src/ffindex_modify.c 2012-01-24 18:13:02.000000000 +0100 +--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_modify.c 2012-02-22 10:33:59.131044487 +0100 ++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c 2012-02-22 10:34:01.431044580 +0100 @@ -30,7 +30,7 @@ void usage(char *program_name) @@ -58,26 +58,26 @@ } int main(int argn, char **argv) -Index: hhsuite-2.0.5/src/hhblits.C +Index: hhsuite-2.0.12/src/hhblits.C =================================================================== ---- hhsuite-2.0.5.orig/src/hhblits.C 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/src/hhblits.C 2012-01-24 19:18:31.140242837 +0100 -@@ -410,8 +410,8 @@ - printf("\n"); - printf("Directory paths \n"); - //printf(" -cs <file> compute context-specific pseudocounts with context library (def=off)\n"); +--- hhsuite-2.0.12.orig/src/hhblits.C 2012-02-22 10:33:59.155044512 +0100 ++++ hhsuite-2.0.12/src/hhblits.C 2012-02-22 10:34:01.443044553 +0100 +@@ -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(" -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"); -@@ -486,7 +486,12 @@ - printf("(The -cpu option is inactive since POSIX threads are not supported on your platform)\n"); - #endif - printf("\n\n"); -- printf("Example: %s -i query.fas -oa3m query.a3m -n 2\n",program_name); +@@ -407,7 +407,12 @@ + 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"); @@ -87,11 +87,11 @@ cout<<endl; } -Index: hhsuite-2.0.5/src/hhsearch.C +Index: hhsuite-2.0.12/src/hhsearch.C =================================================================== ---- hhsuite-2.0.5.orig/src/hhsearch.C 2012-01-20 15:36:45.000000000 +0100 -+++ hhsuite-2.0.5/src/hhsearch.C 2012-01-24 18:13:02.000000000 +0100 -@@ -321,7 +321,7 @@ +--- hhsuite-2.0.12.orig/src/hhsearch.C 2012-02-22 10:33:59.178967644 +0100 ++++ hhsuite-2.0.12/src/hhsearch.C 2012-02-22 10:34:01.451044569 +0100 +@@ -326,7 +326,7 @@ 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!! @@ -100,11 +100,11 @@ 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); } -Index: hhsuite-2.0.5/scripts/HHPaths.pm +Index: hhsuite-2.0.12/scripts/HHPaths.pm =================================================================== ---- hhsuite-2.0.5.orig/scripts/HHPaths.pm 2012-01-24 18:36:53.540242690 +0100 -+++ hhsuite-2.0.5/scripts/HHPaths.pm 2012-01-24 18:46:17.068242762 +0100 -@@ -39,7 +39,7 @@ +--- hhsuite-2.0.12.orig/scripts/HHPaths.pm 2012-02-22 10:33:59.227044558 +0100 ++++ hhsuite-2.0.12/scripts/HHPaths.pm 2012-02-22 10:34:01.459044633 +0100 +@@ -38,7 +38,7 @@ # The lines below probably do not need to be changed # Setting paths for hh-suite perl scripts @@ -113,11 +113,11 @@ 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-2.0.5/src/Makefile +Index: hhsuite-2.0.12/src/Makefile =================================================================== ---- hhsuite-2.0.5.orig/src/Makefile 2012-01-24 19:04:04.092243000 +0100 -+++ hhsuite-2.0.5/src/Makefile 2012-01-24 19:09:35.160242815 +0100 -@@ -76,7 +76,7 @@ +--- hhsuite-2.0.12.orig/src/Makefile 2012-02-22 10:33:59.203044519 +0100 ++++ hhsuite-2.0.12/src/Makefile 2012-02-22 10:34:01.467044453 +0100 +@@ -92,7 +92,7 @@ $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS) hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS) @@ -126,10 +126,10 @@ hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS) $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a -Index: hhsuite-2.0.5/scripts/addss.pl +Index: hhsuite-2.0.12/scripts/addss.pl =================================================================== ---- hhsuite-2.0.5.orig/scripts/addss.pl 2012-01-24 19:37:41.484242639 +0100 -+++ hhsuite-2.0.5/scripts/addss.pl 2012-01-24 19:38:44.556242323 +0100 +--- hhsuite-2.0.12.orig/scripts/addss.pl 2012-02-22 10:33:59.247044552 +0100 ++++ hhsuite-2.0.12/scripts/addss.pl 2012-02-22 10:34:01.471044421 +0100 @@ -28,7 +28,7 @@ # We are very grateful for bug reports! Please contact us at [email protected] @@ -139,10 +139,10 @@ 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 /; -Index: hhsuite-2.0.5/scripts/hhblitsdb.pl +Index: hhsuite-2.0.12/scripts/hhblitsdb.pl =================================================================== ---- hhsuite-2.0.5.orig/scripts/hhblitsdb.pl 2012-01-24 19:37:41.640241898 +0100 -+++ hhsuite-2.0.5/scripts/hhblitsdb.pl 2012-01-24 19:39:07.912242819 +0100 +--- hhsuite-2.0.12.orig/scripts/hhblitsdb.pl 2012-02-22 10:33:59.271044501 +0100 ++++ hhsuite-2.0.12/scripts/hhblitsdb.pl 2012-02-22 10:34:01.479044570 +0100 @@ -28,7 +28,7 @@ # We are very grateful for bug reports! Please contact us at [email protected] @@ -152,10 +152,10 @@ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc. use strict; -Index: hhsuite-2.0.5/scripts/hhmakemodel.pl +Index: hhsuite-2.0.12/scripts/hhmakemodel.pl =================================================================== ---- hhsuite-2.0.5.orig/scripts/hhmakemodel.pl 2012-01-24 19:37:41.684243152 +0100 -+++ hhsuite-2.0.5/scripts/hhmakemodel.pl 2012-01-24 19:39:29.980242773 +0100 +--- hhsuite-2.0.12.orig/scripts/hhmakemodel.pl 2012-02-22 10:33:59.299044594 +0100 ++++ hhsuite-2.0.12/scripts/hhmakemodel.pl 2012-02-22 10:34:01.487044455 +0100 @@ -28,7 +28,7 @@ # We are very grateful for bug reports! Please contact us at [email protected] Modified: trunk/packages/hhsuite/trunk/debian/rules =================================================================== --- trunk/packages/hhsuite/trunk/debian/rules 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/rules 2012-02-22 11:20:09 UTC (rev 9750) @@ -40,3 +40,7 @@ override_dh_clean: rm -f $(FFMANPAGES) $(HHMANPAGES) dh_clean + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs Modified: trunk/packages/hhsuite/trunk/debian/upstream =================================================================== --- trunk/packages/hhsuite/trunk/debian/upstream 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/upstream 2012-02-22 11:20:09 UTC (rev 9750) @@ -3,7 +3,7 @@ Homepage: http://toolkit.genzentrum.lmu.de/hhblits Reference: Author: Remmert M., Biegert A., Hauser A., and Soding J. - Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. ' + Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.' Journal: Nat. Methods DOI: 10.1038/NMETH.1818. year: 2011 Modified: trunk/packages/hhsuite/trunk/debian/watch =================================================================== --- trunk/packages/hhsuite/trunk/debian/watch 2012-02-22 10:46:19 UTC (rev 9749) +++ trunk/packages/hhsuite/trunk/debian/watch 2012-02-22 11:20:09 UTC (rev 9750) @@ -1,3 +1,3 @@ version=3 -ftp://toolkit.lmb.uni-muenchen.de/HH-suite/hhsuite-([0-9.]+)\.tar\.gz debian uupdate +ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/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
