[med-svn] r9419 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Jan 24 18:44:11 UTC 2012
Author: lkajan-guest
Date: 2012-01-24 18:44:10 +0000 (Tue, 24 Jan 2012)
New Revision: 9419
Added:
trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml
Modified:
trunk/packages/hhsuite/trunk/debian/README.source
trunk/packages/hhsuite/trunk/debian/changelog
trunk/packages/hhsuite/trunk/debian/patches/Makefile
trunk/packages/hhsuite/trunk/debian/patches/default_path
trunk/packages/hhsuite/trunk/debian/rules
Log:
added upstream-metadata.yaml, updated upstream version to 2.0.5
Modified: trunk/packages/hhsuite/trunk/debian/README.source
===================================================================
--- trunk/packages/hhsuite/trunk/debian/README.source 2012-01-24 18:29:23 UTC (rev 9418)
+++ trunk/packages/hhsuite/trunk/debian/README.source 2012-01-24 18:44:10 UTC (rev 9419)
@@ -4,7 +4,14 @@
Patches
.......
-patch1:
-* ?
+Makefile:
+* makes Makefile DESTDIR-aware
+* uses $(MAKE) -C for making in subdirectories
+* fixes install mode of data files
+* deinstall -> uninstall
+default_path:
+* fixes issues where the path in help pages is taken from the build-time
+ location of the executables
+
# vim:et:ts=2:
Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog 2012-01-24 18:29:23 UTC (rev 9418)
+++ trunk/packages/hhsuite/trunk/debian/changelog 2012-01-24 18:44:10 UTC (rev 9419)
@@ -1,4 +1,4 @@
-hhsuite (2.0.4-1) UNRELEASED; urgency=low
+hhsuite (2.0.5-1) UNRELEASED; urgency=low
* Initial release (Closes: #656626)
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-01-24 18:29:23 UTC (rev 9418)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-01-24 18:44:10 UTC (rev 9419)
@@ -1,7 +1,7 @@
-Index: hhsuite-2.0.4/Makefile
+Index: hhsuite-2.0.5/Makefile
===================================================================
---- hhsuite-2.0.4.orig/Makefile 2012-01-20 10:54:23.000000000 +0100
-+++ hhsuite-2.0.4/Makefile 2012-01-23 15:39:20.036242021 +0100
+--- hhsuite-2.0.5.orig/Makefile 2012-01-20 15:36:45.000000000 +0100
++++ hhsuite-2.0.5/Makefile 2012-01-24 18:05:59.980241952 +0100
@@ -1,5 +1,5 @@
# This can be overridden e.g.: make install INSTALL_DIR=...
-INSTALL_DIR?=$(PWD)
@@ -19,7 +19,7 @@
INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data
INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
- dist_name=hhsuite-2.0.4
+ dist_name=hhsuite-2.0.5
-all_static: ffindex_static
- cd src && make all_static
@@ -106,10 +106,10 @@
dist/$(dist_name).tar.gz:
make clean
-Index: hhsuite-2.0.4/scripts/HHPaths.pm
+Index: hhsuite-2.0.5/scripts/HHPaths.pm
===================================================================
---- hhsuite-2.0.4.orig/scripts/HHPaths.pm 2012-01-20 10:54:23.000000000 +0100
-+++ hhsuite-2.0.4/scripts/HHPaths.pm 2012-01-23 11:31:41.000000000 +0100
+--- 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 @@
# The lines below probably do not need to be changed
@@ -119,10 +119,10 @@
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
+Index: hhsuite-2.0.5/src/hhdecl.C
===================================================================
---- hhsuite-2.0.4.orig/src/hhdecl.C 2012-01-20 10:54:23.000000000 +0100
-+++ hhsuite-2.0.4/src/hhdecl.C 2012-01-23 16:22:16.328242836 +0100
+--- 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 @@
if(getenv("HHLIB"))
strcpy(hhlib, getenv("HHLIB"));
@@ -150,10 +150,10 @@
exit(2);
}
-Index: hhsuite-2.0.4/lib/ffindex/Makefile
+Index: hhsuite-2.0.5/lib/ffindex/Makefile
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/Makefile 2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.4/lib/ffindex/Makefile 2012-01-23 11:31:41.000000000 +0100
+--- 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
@@ -7,13 +7,7 @@
endif
@@ -171,10 +171,10 @@
- cd src ; make clean
+%:
+ $(MAKE) -C src $@
-Index: hhsuite-2.0.4/lib/ffindex/src/Makefile
+Index: hhsuite-2.0.5/lib/ffindex/src/Makefile
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/src/Makefile 2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.4/lib/ffindex/src/Makefile 2012-01-23 11:31:41.000000000 +0100
+--- 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
@@ -1,12 +1,14 @@
INSTALL_DIR?=..
-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
@@ -240,10 +240,10 @@
rmdir $(INSTALL_DIR)/bin || true
rmdir $(INSTALL_DIR)/$(libdir) || true
rmdir $(INSTALL_DIR)/include || true
-Index: hhsuite-2.0.4/src/Makefile
+Index: hhsuite-2.0.5/src/Makefile
===================================================================
---- hhsuite-2.0.4.orig/src/Makefile 2012-01-20 10:54:23.000000000 +0100
-+++ hhsuite-2.0.4/src/Makefile 2012-01-23 11:31:41.000000000 +0100
+--- hhsuite-2.0.5.orig/src/Makefile 2012-01-20 15:36:45.000000000 +0100
++++ hhsuite-2.0.5/src/Makefile 2012-01-24 17:57:52.660242672 +0100
@@ -31,7 +31,7 @@
ifeq ($(OS), Linux)
HHSEARCH_LIBS = -lpthread -lrt
Modified: trunk/packages/hhsuite/trunk/debian/patches/default_path
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-01-24 18:29:23 UTC (rev 9418)
+++ trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-01-24 18:44:10 UTC (rev 9419)
@@ -1,7 +1,7 @@
-Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_build.c
+Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_build.c
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_build.c 2012-01-23 18:03:01.532243170 +0100
-+++ hhsuite-2.0.4/lib/ffindex/src/ffindex_build.c 2012-01-23 18:05:51.100242425 +0100
+--- 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
@@ -31,7 +31,7 @@
void usage(char *program_name)
@@ -11,23 +11,35 @@
"\t-a\tappend\n"
"\t-d a second ffindex data file for inserting/appending\n"
"\t-i a second ffindex index file for insterting/appending\n"
-Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_get.c
+@@ -39,7 +39,7 @@
+ "\t\t-f can be specified up to %d times\n"
+ "\t-s\tsort index file\n"
+ "\t-v\tprint version and other info then exit\n"
+- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", program_name, MAX_FILENAME_LIST_FILES);
++ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", MAX_FILENAME_LIST_FILES);
+ }
+
+ int main(int argn, char **argv)
+Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_get.c
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_get.c 2012-01-23 18:03:01.616245335 +0100
-+++ hhsuite-2.0.4/lib/ffindex/src/ffindex_get.c 2012-01-23 18:06:33.956242514 +0100
-@@ -26,7 +26,7 @@
+--- 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
+@@ -26,9 +26,8 @@
{
if(argn < 3)
{
- fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n"
+- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
+- argv[0]);
+ fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n"
- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
- argv[0]);
++ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n");
return -1;
-Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_modify.c
+ }
+ char *data_filename = argv[1];
+Index: hhsuite-2.0.5/lib/ffindex/src/ffindex_modify.c
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_modify.c 2012-01-23 18:03:01.576242602 +0100
-+++ hhsuite-2.0.4/lib/ffindex/src/ffindex_modify.c 2012-01-23 18:06:10.340241903 +0100
+--- 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
@@ -30,7 +30,7 @@
void usage(char *program_name)
@@ -37,10 +49,19 @@
"\t-f file\tfile each line containing a filename\n"
"\t\t-f can be specified up to %d times\n"
"\t-s\tsort index file\n"
-Index: hhsuite-2.0.4/src/hhblits.C
+@@ -38,7 +38,7 @@
+ "\t-u\tunlink entry (remove from index only)\n"
+ "\t-v\tprint version and other info then exit\n"
+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
+- program_name, MAX_FILENAME_LIST_FILES);
++ MAX_FILENAME_LIST_FILES);
+ }
+
+ int main(int argn, char **argv)
+Index: hhsuite-2.0.5/src/hhblits.C
===================================================================
---- hhsuite-2.0.4.orig/src/hhblits.C 2012-01-23 17:50:34.640245145 +0100
-+++ hhsuite-2.0.4/src/hhblits.C 2012-01-23 18:01:36.584242765 +0100
+--- 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");
@@ -52,10 +73,24 @@
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");
-Index: hhsuite-2.0.4/src/hhsearch.C
+@@ -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);
++ 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;
+ }
+
+Index: hhsuite-2.0.5/src/hhsearch.C
===================================================================
---- hhsuite-2.0.4.orig/src/hhsearch.C 2012-01-23 17:50:34.684242434 +0100
-+++ hhsuite-2.0.4/src/hhsearch.C 2012-01-23 18:02:22.412243167 +0100
+--- 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 @@
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);
@@ -65,3 +100,68 @@
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
+===================================================================
+--- 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 @@
+ # The lines below probably do not need to be changed
+
+ # Setting paths for hh-suite perl scripts
+-our $hhlib = "/usr/lib/hhsuite"; # main hh-suite directory
++our $hhlib = $ENV{"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-2.0.5/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 @@
+ $(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) $(HHBLITS_LIBS) -lffindex -L$(FFINDEX_DIR)
+
+ 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
+===================================================================
+--- 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
+@@ -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/lib/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 /;
+Index: hhsuite-2.0.5/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
+@@ -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/lib/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+Index: hhsuite-2.0.5/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
+@@ -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/lib/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use Align;
Modified: trunk/packages/hhsuite/trunk/debian/rules
===================================================================
--- trunk/packages/hhsuite/trunk/debian/rules 2012-01-24 18:29:23 UTC (rev 9418)
+++ trunk/packages/hhsuite/trunk/debian/rules 2012-01-24 18:44:10 UTC (rev 9419)
@@ -3,15 +3,14 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
-VERSION=2.0.4
+VERSION=2.0.5
%:
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)'
+ #'$(MAKE)' '$(MAKEFLAGS)' '$(DEB_BUILD_OPTIONS)'
parallel=1 && eval $(DEB_BUILD_OPTIONS) && make -j$$parallel
.PHONY: override_dh_strip
@@ -40,7 +39,7 @@
unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
- export HHLIB=debian/tmp/usr/lib/hhsuite && eval '$(BINNAMES)' && help2man --no-info '--help-option=-h all' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
+ unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/lib/hhsuite && eval '$(BINNAMES)' && help2man --no-info '--help-option=-h all' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
.PHONY: override_dh_clean
override_dh_clean:
Added: trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml 2012-01-24 18:44:10 UTC (rev 9419)
@@ -0,0 +1,19 @@
+Name: hhsuite
+Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
+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. '
+ Journal: Nat. Methods
+ DOI: 10.1038/NMETH.1818.
+ year: 2011
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/22198341
+ PMID: 22198341
+ - Author: Soding J.
+ Title: Protein homology detection by HMM-HMM comparison.
+ Journal: Bioinformatics
+ Volume: 21
+ Pages: 951-960
+ Year: 2005
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/15531603
+ PMID: 15531603
More information about the debian-med-commit
mailing list