Author: lkajan Date: 2013-05-23 09:38:56 +0000 (Thu, 23 May 2013) New Revision: 13701
Added: trunk/packages/hhsuite/trunk/debian/patches/perl_interpreter trunk/packages/hhsuite/trunk/debian/patches/perlscript_uselib Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile trunk/packages/hhsuite/trunk/debian/patches/hardening trunk/packages/hhsuite/trunk/debian/patches/help trunk/packages/hhsuite/trunk/debian/patches/paths trunk/packages/hhsuite/trunk/debian/patches/rest1 trunk/packages/hhsuite/trunk/debian/patches/series Log: upstream 2.0.16-1 builds correctly, but package is yet untested Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2013-05-23 09:38:56 UTC (rev 13701) @@ -27,7 +27,7 @@ +INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin - dist_name=hhsuite-2.0.15 + dist_name=hhsuite-2.0.16 -.PHONY: all_static -all_static: ffindex_static Modified: trunk/packages/hhsuite/trunk/debian/patches/hardening =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/hardening 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/hardening 2013-05-23 09:38:56 UTC (rev 13701) @@ -2,19 +2,12 @@ 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$(CS_DIR) -+ CXXFLAGS += -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) - HHSEARCH_LIBS = -lpthread -lrt - HHBLITS_LIBS = -lpthread -lrt -openmp +@@ -20,7 +20,7 @@ OBJECT_LIBS = -openmp else # ifndef ICC CXX = g++ -- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -+ CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) +- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp ++ CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp HHSEARCH_LIBS = -lpthread HHBLITS_LIBS = -lpthread -fopenmp HHALIGN_LIBS = Modified: trunk/packages/hhsuite/trunk/debian/patches/help =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/help 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/help 2013-05-23 09:38:56 UTC (rev 13701) @@ -4,7 +4,7 @@ Author: Laszlo Kajan <[email protected]> --- a/src/hhblits.C +++ b/src/hhblits.C -@@ -382,8 +382,8 @@ +@@ -381,8 +381,8 @@ printf("\n"); printf("Context-specific pseudo-counts: \n"); printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); @@ -15,7 +15,7 @@ printf("\n"); printf("Predict secondary structure\n"); printf(" -addss add 2ndary structure predicted with PSIPRED to result MSA \n"); -@@ -412,7 +412,12 @@ +@@ -411,7 +411,12 @@ printf("An extended list of options can be obtained by calling 'hhblits -help'\n"); } printf("\n"); @@ -25,13 +25,13 @@ + 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"); ++ printf("Download databases from <ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/databases/>.\n"); cout<<endl; } --- a/src/hhsearch.C +++ b/src/hhsearch.C -@@ -41,6 +41,7 @@ +@@ -48,6 +48,7 @@ #include <float.h> // FLT_MIN #include <ctype.h> // islower, isdigit etc #include <time.h> // clock_gettime etc. (in realtime library (-lrt compiler option)) @@ -39,7 +39,7 @@ #include <errno.h> // perror() #include <cassert> #include <stdexcept> -@@ -300,8 +301,8 @@ +@@ -308,8 +309,8 @@ printf("\n"); printf("Context-specific pseudo-counts: \n"); printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); Modified: trunk/packages/hhsuite/trunk/debian/patches/paths =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/paths 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/paths 2013-05-23 09:38:56 UTC (rev 13701) @@ -4,16 +4,15 @@ Author: Laszlo Kajan <[email protected]> --- a/scripts/HHPaths.pm +++ b/scripts/HHPaths.pm -@@ -30,7 +30,7 @@ - use Exporter; - our $VERSION = "version 2.0.15 (June 2012)"; +@@ -31,6 +31,7 @@ + our $VERSION = "version 2.0.16 (January 2013)"; our @ISA = qw(Exporter); --our @EXPORT = qw($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 $context_lib); + our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v); ++push @EXPORT, qw($hhshare $hhbdata); ############################################################################################## # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) -@@ -54,11 +54,13 @@ +@@ -54,11 +55,13 @@ # The lines below probably do not need to be changed # Setting paths for hh-suite perl scripts Added: trunk/packages/hhsuite/trunk/debian/patches/perl_interpreter =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/perl_interpreter (rev 0) +++ trunk/packages/hhsuite/trunk/debian/patches/perl_interpreter 2013-05-23 09:38:56 UTC (rev 13701) @@ -0,0 +1,91 @@ +Description: patch Perl interpreter as required by Polich 5.1 + Perl Script Magic - http://www.debian.org/doc/packaging-manuals/perl-policy/ch-programs.html#s-hash_bang +Author: Laszlo Kajan <[email protected]> +--- a/scripts/addss.pl ++++ b/scripts/addss.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # + # addss.pl + # Add PSIPRED secondary structure prediction (and DSSP annotation) to an MSA or HMMER file. +--- a/scripts/create_profile_from_hhm.pl ++++ b/scripts/create_profile_from_hhm.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # + # create_profile_from_hhm.pl + # Create a profile (.prf) from a given HHM file +--- a/scripts/create_profile_from_hmmer.pl ++++ b/scripts/create_profile_from_hmmer.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # + # create_profile_from_hmmer.pl + # Create a profile (.prf) from a given HMMER/HMMER3 file +--- a/scripts/hhblitsdb.pl ++++ b/scripts/hhblitsdb.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # + # hhblits.pl + # Creates HH-suite database files from A3M and HHM/HMMER-formatted files +--- a/scripts/hhmakemodel.pl ++++ b/scripts/hhmakemodel.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/env perl ++#!/usr/bin/perl + # + # hhmakemodel.pl + # Generate a model from an output alignment of hhsearch. +--- a/scripts/multithread.pl ++++ b/scripts/multithread.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # + # multithread.pl: + # Run a command with different file names as arguments on multiple threads in parallel +--- a/scripts/pdb2fasta.pl ++++ b/scripts/pdb2fasta.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/env perl ++#!/usr/bin/perl + # + # pdb2fasta.pl - generate FASTA nonredundant sequence file from SEQRES records of globbed pdb files. + +--- a/scripts/pdbfilter.pl ++++ b/scripts/pdbfilter.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/env perl ++#!/usr/bin/perl + # pdbfilter.pl - Read pdb or SCOP sequences from infile and write representative set of sequences to outfile + + # +--- a/scripts/reformat.pl ++++ b/scripts/reformat.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/env perl ++#!/usr/bin/perl + + # reformat.pl + # Reformat a multiple alignment file +--- a/scripts/renumberpdb.pl ++++ b/scripts/renumberpdb.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + # renumberpdb.pl - generate a PDB file with renumbered indices that match residue indices in input sequence + # Usage: renumberpdb.pl [options] infile [outfile] + # Example: renumberpdb.pl d1hz4a_.a3m d1hz4a_.pdb +--- a/scripts/splitfasta.pl ++++ b/scripts/splitfasta.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/env perl ++#!/usr/bin/perl + # splitfasta.pl + # Split a file with multiple, FASTA formatted sequences into many single-sequence FASTA files + # Added: trunk/packages/hhsuite/trunk/debian/patches/perlscript_uselib =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/perlscript_uselib (rev 0) +++ trunk/packages/hhsuite/trunk/debian/patches/perlscript_uselib 2013-05-23 09:38:56 UTC (rev 13701) @@ -0,0 +1,124 @@ +Description: Perl script use lib + * Set paths to hhsuite components for Perl scripts. +Author: Laszlo Kajan <[email protected]> +--- a/scripts/addss.pl ++++ b/scripts/addss.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 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; + #use File::Glob 'bsd_glob'; # splits patterns delimited by spaces into multiple patterns and applies them using OR +--- 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; +--- 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; +--- a/scripts/pdb2fasta.pl ++++ b/scripts/pdb2fasta.pl +@@ -26,7 +26,7 @@ + + # 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; + $|= 1; # Activate autoflushing on STDOUT +--- a/scripts/pdbfilter.pl ++++ b/scripts/pdbfilter.pl +@@ -26,7 +26,7 @@ + + # 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/renumberpdb.pl ++++ b/scripts/renumberpdb.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 Align; # Needleman-Wunsch and Smith-Waterman alignment functions + use strict; +--- a/scripts/splitfasta.pl ++++ b/scripts/splitfasta.pl +@@ -26,7 +26,7 @@ + + # We are very grateful for bug reports! Please contact us at [email protected] + +-use lib $ENV{"HHLIB"}."/scripts"; ++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts"; + use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc. + use strict; + use warnings; Modified: trunk/packages/hhsuite/trunk/debian/patches/rest1 =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/rest1 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/rest1 2013-05-23 09:38:56 UTC (rev 13701) @@ -1,5 +1,4 @@ Description: Assorted patches - * Set paths to hhsuite components for Perl scripts. * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq . Author: Laszlo Kajan <[email protected]> --- a/src/Makefile @@ -15,8 +14,8 @@ OBJECT_LIBS = -openmp else # ifndef ICC CXX = g++ -- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -+ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) +- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -fopenmp ++ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp HHSEARCH_LIBS = -lpthread HHBLITS_LIBS = -lpthread -fopenmp HHALIGN_LIBS = @@ -29,39 +28,6 @@ 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 @@ @@ -76,47 +42,3 @@ + +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 2013-05-23 07:12:23 UTC (rev 13700) +++ trunk/packages/hhsuite/trunk/debian/patches/series 2013-05-23 09:38:56 UTC (rev 13701) @@ -2,6 +2,8 @@ paths help rest1 +perlscript_uselib hardening unused_variables_warning unnecessary_libz +perl_interpreter _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
