[med-svn] r9750 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed Feb 22 11:20:09 UTC 2012
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 <lkajan at rostlab.org> Fri, 20 Jan 2012 15:10:40 +0100
+ -- Laszlo Kajan <lkajan at rostlab.org> 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 soeding at genzentrum.lmu.de
@@ -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 soeding at genzentrum.lmu.de
@@ -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 soeding at genzentrum.lmu.de
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
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