debian/0000755000000000000000000000000012223013215007155 5ustar debian/watch0000644000000000000000000000017412034237232010217 0ustar version=3 opts=passive \ ftp://toolkit.lmb.uni-muenchen.de/pub/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz debian uupdate debian/hhsuite.links0000644000000000000000000000003411721737224011704 0ustar /usr/lib/hhsuite usr/lib/hh debian/README.source0000644000000000000000000000016011721204364011342 0ustar hhsuite for Debian ------------------ Patches ....... Patches are documented in their headers. # vim:et:ts=2: debian/hhsuite.examples0000644000000000000000000000001511721737224012401 0ustar data/query.* debian/hhsuite.install0000644000000000000000000000006511721737224012236 0ustar usr/bin/hh* usr/lib/hhsuite/bin usr/lib/hhsuite/data debian/rules0000755000000000000000000000332512147340527010256 0ustar #!/usr/bin/make -f export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 VERSION=$(shell sed --posix -n -e '/VERSION_AND_DATE/{ s/.*version \([0-9][0-9.]*\).*/\1/; p; }' src/hhdecl.C) HHMANPAGES = hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 export n_hhalign=align a query alignment/HMM to a template alignment/HMM export n_hhblits=fast homology detection method to iteratively search a HMM database export n_hhconsensus=calculate the consensus sequence for an A3M/FASTA input file export n_hhfilter=filter an alignment by maximum sequence identity of match states and minimum coverage export n_hhmake=build an HMM from an input alignment or convert between HMMER format and HHsearch format export n_hhsearch=search a database of HMMs with a query alignment or query HMM .PHONY: hhmanpages hhmanpages: $(HHMANPAGES) .PHONY: override_dh_strip override_dh_strip: dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so .PHONY: override_dh_installman override_dh_installman: $(HHMANPAGES) dh_installman $(HHMANPAGES): %.1 : debian/tmp/usr/bin/% unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@' .PHONY: override_dh_clean override_dh_clean: rm -f $(HHMANPAGES) dh_clean get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs %: dh $@ --parallel debian/hhsuite-data.links0000644000000000000000000000030011721737224012607 0ustar usr/share/hhsuite/scripts usr/lib/hhsuite/scripts usr/share/hhsuite/data/context_data.lib usr/lib/hhsuite/data/context_data.lib usr/share/hhsuite/data/cs219.lib usr/lib/hhsuite/data/cs219.lib debian/hhsuite-data.install0000644000000000000000000000006111721737224013141 0ustar usr/share/hhsuite/data usr/share/hhsuite/scripts debian/hhsuite.doc-base0000644000000000000000000000042411721147551012242 0ustar 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 debian/hhsuite.docs0000644000000000000000000000003511721410664011511 0ustar hhsuite-userguide.pdf README debian/hhsuite.manpages0000644000000000000000000000010111707312144012344 0ustar hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 debian/copyright0000644000000000000000000000646211772617264011146 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: hhsuite Upstream-Contact: Andreas Hauser Johannes Soeding Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz Files: src/fmemopen.c src/fmemopen.h lib/ffindex/src/ext/fmemopen.c lib/ffindex/src/ext/fmemopen.h Copyright: 2009 Open Information Security Foundation License: GPL-2.0+ Files: src/cs/getopt_pp.h src/cs/getopt_pp.cc Copyright: 2007, 2008 Daniel Gutson, FuDePAN License: GPL-3.0+ Files: src/pngwriter.cc src/pngwriter.h Copyright: 2002, 2003 Paul Blackburn License: GPL-2.0+ Files: lib/ffindex/* Copyright: Andy Hauser License: CC-BY-SA-3.0 Files: debian/* Copyright: 2012 Laszlo Kajan License: GPL-3.0+ Files: * Copyright: 2006, 2012 Johannes Soeding 2012 Michael Remmert 2012 Andreas Hauser 2006, 2009, 2012 Andreas Biegert License: GPL-3.0+ License: CC-BY-SA-3.0 Create Commons license "Attribution-ShareAlike 3.0" . See: http://creativecommons.org/licenses/by-sa/3.0/ . Basically you are free: . * to Share — to copy, distribute and transmit the work * to Remix — to adapt the work . Under the following conditions: . * Attribution You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). * Share Alike If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one. License: GPL-2.0+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: GPL-3.0+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/upstream0000644000000000000000000000157711752035327010770 0ustar Name: hhsuite Contact: Andreas Hauser Homepage: http://toolkit.genzentrum.lmu.de/hhblits Reference: - Author: Michael Remmert and Andreas Biegert and Andreas Hauser and Johannes Söding Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.' Journal: Nat. Methods DOI: 10.1038/NMETH.1818 Year: 2011 Volume: 9 Number: 2 Pages: 173-175 URL: http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1818.html PMID: 22198341 - Author: Johannes Söding Title: Protein homology detection by HMM-HMM comparison. Journal: Bioinformatics Volume: 21 Number: 7 Pages: 951-960 Year: 2005 PMID: 15531603 DOI: 10.1093/bioinformatics/bti125 URL: http://bioinformatics.oxfordjournals.org/content/21/7/951.abstract eprint: http://bioinformatics.oxfordjournals.org/content/21/7/951.full.pdf+htmldebian/docs0000644000000000000000000000003511707312144010037 0ustar README hhsuite-userguide.pdf debian/source/0000755000000000000000000000000012147403654010474 5ustar debian/source/format0000644000000000000000000000001411706353162011700 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012147403656010625 5ustar debian/patches/rest10000644000000000000000000000345012147361660011606 0ustar Description: Assorted patches * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq . Author: Laszlo Kajan --- 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) -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 = @@ -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 --- /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 debian/patches/perlscript_uselib0000644000000000000000000001103212147361660014275 0ustar Description: Perl script use lib * Set paths to hhsuite components for Perl scripts. Author: Laszlo Kajan --- a/scripts/addss.pl +++ b/scripts/addss.pl @@ -29,7 +29,7 @@ # We are very grateful for bug reports! Please contact us at soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -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 soeding@genzentrum.lmu.de -use lib $ENV{"HHLIB"}."/scripts"; +use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts"; use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc. use strict; use warnings; debian/patches/Makefile0000644000000000000000000001261412147361660012267 0ustar Description: Patch to top level Makefile * Make Makefile DESTDIR-aware. * Fix install mode of data files. Forwarded: upstream is aware of these patches Upstream is Andreas Hauser . Author: Laszlo Kajan --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ -# This can be overridden e.g.: make install INSTALL_DIR=... -INSTALL_DIR?=$(PWD) +# This can be overridden e.g.: make install PREFIX=... +PREFIX:=/usr # Guess wether to use lib or lib64 #libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib` @@ -8,19 +8,17 @@ # Overriding this is currently not fully supported as the code won't know # to what this is set then. You can try setting HHLIB. -INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hh -INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts -INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data +INSTALL_LIB_DIR?=$(PREFIX)/$(libdir)/hhsuite +INSTALL_SCRIPTS_DIR?=$(PREFIX)/share/hhsuite/scripts +INSTALL_DATA_DIR?=$(PREFIX)/share/hhsuite/data +INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin dist_name=hhsuite-2.0.16 -.PHONY: all_static -all_static: ffindex_static - $(MAKE) -C src all_static - .PHONY: all -all: ffindex +all: + $(MAKE) -C data all $(MAKE) -C src all doc: @@ -40,35 +38,34 @@ $(MAKE) -C lib/ffindex FFINDEX_STATIC=1 install: - $(MAKE) -C lib/ffindex install INSTALL_DIR=$(INSTALL_DIR) - mkdir -p $(INSTALL_DIR)/bin - install src/hhblits $(INSTALL_DIR)/bin/hhblits - install src/hhalign $(INSTALL_DIR)/bin/hhalign - install src/hhconsensus $(INSTALL_DIR)/bin/hhconsensus - install src/hhfilter $(INSTALL_DIR)/bin/hhfilter - install src/hhmake $(INSTALL_DIR)/bin/hhmake - install src/hhsearch $(INSTALL_DIR)/bin/hhsearch - mkdir -p $(INSTALL_LIB_DIR) - mkdir -p $(INSTALL_LIB_BIN_DIR) - install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate - mkdir -p $(INSTALL_DATA_DIR) - install -m 0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib - install -m 0644 data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib - install -m 0644 data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete - install -m 0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr - install -m 0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin - install -m 0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq - mkdir -p $(INSTALL_SCRIPTS_DIR) - install -m 0644 scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm - install -m 0644 scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm - 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 - install scripts/splitfasta.pl $(INSTALL_SCRIPTS_DIR)/splitfasta.pl - install scripts/multithread.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl - install scripts/hhblitsdb.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl + mkdir -p $(DESTDIR)$(PREFIX)/bin + install src/hhblits $(DESTDIR)$(PREFIX)/bin/hhblits + install src/hhalign $(DESTDIR)$(PREFIX)/bin/hhalign + install src/hhconsensus $(DESTDIR)$(PREFIX)/bin/hhconsensus + install src/hhfilter $(DESTDIR)$(PREFIX)/bin/hhfilter + install src/hhmake $(DESTDIR)$(PREFIX)/bin/hhmake + install src/hhsearch $(DESTDIR)$(PREFIX)/bin/hhsearch + mkdir -p $(DESTDIR)$(INSTALL_LIB_DIR) + mkdir -p $(DESTDIR)$(INSTALL_LIB_BIN_DIR) + install src/cstranslate $(DESTDIR)$(INSTALL_LIB_BIN_DIR)/cstranslate + mkdir -p $(DESTDIR)$(INSTALL_DATA_DIR) $(DESTDIR)$(INSTALL_BDATA_DIR) + install --mode=0644 data/context_data.lib $(DESTDIR)$(INSTALL_DATA_DIR)/context_data.lib + install --mode=0644 data/cs219.lib $(DESTDIR)$(INSTALL_DATA_DIR)/cs219.lib + install --mode=0644 data/do_not_delete $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete + install --mode=0644 data/do_not_delete.phr $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.phr + install --mode=0644 data/do_not_delete.pin $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.pin + install --mode=0644 data/do_not_delete.psq $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.psq + mkdir -p $(DESTDIR)$(INSTALL_SCRIPTS_DIR) + install --mode=0644 scripts/Align.pm $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/Align.pm + install --mode=0644 scripts/HHPaths.pm $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/HHPaths.pm + install scripts/addss.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/addss.pl + install scripts/create_profile_from_hhm.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl + install scripts/create_profile_from_hmmer.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl + install scripts/hhmakemodel.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl + install scripts/reformat.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/reformat.pl + install scripts/splitfasta.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/splitfasta.pl + install scripts/multithread.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl + install scripts/hhblitsdb.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl deinstall: $(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR) @@ -89,9 +86,11 @@ .PHONY: clean clean: - cd lib/ffindex && $(MAKE) clean $(MAKE) -C src clean +.PHONY: distclean +distclean: clean + dist/$(dist_name).tar.gz: make clean mkdir -p dist debian/patches/perl_interpreter0000644000000000000000000000512712147361660014140 0ustar 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 --- 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 # debian/patches/version_bump0000644000000000000000000000145512147373406013264 0ustar Description: fix version where it is not up to date Author: Laszlo Kajan --- a/src/hhdecl.C +++ b/src/hhdecl.C @@ -10,7 +10,7 @@ //// Constants ///////////////////////////////////////////////////////////////////////////////////// -EXTERN const char VERSION_AND_DATE[]="version 2.0.15 (June 2012)"; +EXTERN const char VERSION_AND_DATE[]="version 2.0.16 (January 2013)"; EXTERN const char REFERENCE[]="Remmert M, Biegert A, Hauser A, and Soding J.\nHHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.\nNat. Methods 9:173-175 (2011).\n"; EXTERN const char COPYRIGHT[]="(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser\n"; EXTERN const int MAXSEQ=65535; //max number of sequences in input alignment (must be <~30000 on cluster nodes??) debian/patches/hardening0000644000000000000000000000123512147361660012506 0ustar Description: Hardening patch. Author: Laszlo Kajan --- a/src/Makefile +++ b/src/Makefile @@ -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) $(BITS_FLAG) -fopenmp + CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp HHSEARCH_LIBS = -lpthread HHBLITS_LIBS = -lpthread -fopenmp HHALIGN_LIBS = @@ -51,7 +51,7 @@ endif endif # ifndef ICC -CPP = $(CXX) $(CXXFLAGS) +CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) CPP_VALGRIND = $(CXX) -g $(CXXFLAGS) debian/patches/unnecessary_libz0000644000000000000000000000057411772616546014144 0ustar Description: remove unnecessary libz link Forwarded: yes Author: Laszlo Kajan --- a/src/Makefile +++ b/src/Makefile @@ -46,7 +46,7 @@ HHSEARCH_LIBS = -lpthread -lrt 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 debian/patches/unused_variables_warning0000644000000000000000000000101711772616546015636 0ustar Description: fix unused variables warning Forwarded: yes Author: Laszlo Kajan --- a/src/pngwriter.cc +++ b/src/pngwriter.cc @@ -3343,13 +3343,13 @@ { std::cerr << " PNGwriter::scale_wh - ERROR **: Negative or zero final width or height not allowed." << std::endl; } - +/* double kx; double ky; kx = ((double)finalwidth)/((double)width_); ky = ((double)finalheight)/((double)height_); - +*/ pngwriter temp(finalwidth, finalheight, 0, "temp"); int red, green, blue; debian/patches/paths0000644000000000000000000000535512147361660011675 0ustar 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 --- a/scripts/HHPaths.pm +++ b/scripts/HHPaths.pm @@ -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 $v); +push @EXPORT, qw($hhshare $hhbdata); ############################################################################################## # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) @@ -54,11 +55,13 @@ # 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 @@ -285,7 +285,7 @@ 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"); @@ -300,7 +300,7 @@ /* 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"); debian/patches/help0000644000000000000000000000560712147361660011506 0ustar 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 --- a/src/hhblits.C +++ b/src/hhblits.C @@ -381,8 +381,8 @@ printf("\n"); printf("Context-specific pseudo-counts: \n"); printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); - printf(" -contxt context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile); - printf(" -cslib column state file for fast database prefiltering (default=%s)\n",par.cs_library); + printf(" -contxt context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n"); + printf(" -cslib 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 result MSA \n"); @@ -411,7 +411,12 @@ 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 \n",program_name); + printf("\n"); + printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d \n",program_name); + printf("\n"); + printf("Download databases from .\n"); cout< // FLT_MIN #include // islower, isdigit etc #include // clock_gettime etc. (in realtime library (-lrt compiler option)) +#include #include // perror() #include #include @@ -308,8 +309,8 @@ printf("\n"); printf("Context-specific pseudo-counts: \n"); printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); - printf(" -contxt context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile); - printf(" -cslib column state file for fast database prefiltering (default=%s)\n",par.cs_library); + printf(" -contxt context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n"); + printf(" -cslib 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); debian/patches/series0000644000000000000000000000017612147373406012045 0ustar Makefile paths help rest1 perlscript_uselib hardening unused_variables_warning unnecessary_libz perl_interpreter version_bump debian/compat0000644000000000000000000000000211706353162010370 0ustar 8 debian/control0000644000000000000000000000504312223013216010563 0ustar Source: hhsuite Section: science Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev Standards-Version: 3.9.3 Homepage: http://toolkit.genzentrum.lmu.de/sections/search Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/ DM-Upload-Allowed: yes Package: hhsuite Architecture: amd64 Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex (>= 0.9.6.1), hhsuite-data (= ${source:Version}) 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 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 homologous templates and to build highly accurate query-template pairwise alignments for homology modeling. . HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. Package: hhsuite-data Architecture: amd64 Depends: ${misc:Depends} Description: sensitive protein sequence searching based on HMM-HMM alignment (data) 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 architecture independent scripts and data files. Package: hhsuite-dbg Architecture: amd64 Section: debug Depends: hhsuite (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} Description: sensitive protein sequence searching based on HMM-HMM alignment (debug) 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. debian/changelog0000644000000000000000000000331612223013215011032 0ustar hhsuite (2.0.16-1ubuntu1) saucy; urgency=low * Make hhsuite-data Architecture: amd64 even though it contains architecture-independent files; it's useless on other architectures, and an Architecture: all package does not get built on Ubuntu build daemons unless either all binary packages are Architecture: all or at least one package builds on i386. -- Colin Watson Wed, 02 Oct 2013 13:50:20 +0100 hhsuite (2.0.16-1) unstable; urgency=low * New upstream release. * Updated d/watch file. -- Laszlo Kajan Mon, 24 Sep 2012 09:32:14 +0200 hhsuite (2.0.15-1) unstable; urgency=low * New upstream release. -- Laszlo Kajan Wed, 27 Jun 2012 14:17:05 +0200 hhsuite (2.0.14-1) unstable; urgency=low * [Andreas Tille ] debian/upstream: Enhanced author values * [Laszlo Kajan ] New upstream release. -- Laszlo Kajan Wed, 23 May 2012 10:52:40 +0200 hhsuite (2.0.13-2) unstable; urgency=low * [Andreas Tille ] debian/upstream: - it is (now) possible to support more than one citation - more verbose citation information * [Laszlo Kajan to src/hhsearch.C in order to fix compilation issue with g++-4.7. (Closes: #667201) -- Laszlo Kajan Wed, 04 Apr 2012 13:45:49 +0200 hhsuite (2.0.13-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Wed, 07 Mar 2012 09:35:48 +0100 hhsuite (2.0.12-1) unstable; urgency=low * Initial release (Closes: #656626) -- Laszlo Kajan Wed, 22 Feb 2012 10:03:00 +0100