debian/0000755000000000000000000000000012171023446007166 5ustar debian/dirs0000644000000000000000000000001010673424515010050 0ustar usr/bin debian/wise-doc.doc-base.api0000644000000000000000000000043311171623372013052 0ustar Document: wise-api Title: Wise API Manual Author: Ewan Birney Abstract: This manual describes the wise API. Section: Science/Biology Format: PDF Files: /usr/share/doc/wise-doc/api.pdf.gz Format: HTML Index: /usr/share/doc/wise-doc/api/api.html Files: /usr/share/doc/wise-doc/api/* debian/README.Debian0000644000000000000000000000050010742717005011225 0ustar wise for Debian -------------------------------------------------------------------------------- You may want to copy /usr/share/doc/wise-doc/examles/* (distributed by wise-doc) to your home directory and set WISECONFIGDIR appropriately. -- Philipp Benner , Mon, 14 Jan 2008 18:36:28 +0100 debian/rules0000755000000000000000000000415012170724745010257 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 # hardening flags DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk %: dh $@ override_dh_auto_build: $(MAKE) -C src all $(MAKE) -C debian/manpages.d # build documentation manually (docs/makefile is not useable) cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex # sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex # cd docs && pdflatex api.tex cd docs && pdflatex api.tex cd docs && pdflatex dynamite.tex cd docs && pdflatex dynamite.tex # cd docs && ps2pdf genewise6.eps # segfaults on s390 # cd docs && ps2pdf genewise21.eps cd docs && pdflatex wise2.tex cd docs && pdflatex wise2.tex cd docs && hevea api.tex cd docs && hevea api.tex cd docs && hevea dynamite.tex cd docs && hevea dynamite.tex cd docs && hevea wise2.tex cd docs && hevea wise2.tex mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build override_dh_clean: $(MAKE) -C src clean $(MAKE) -C debian/manpages.d clean # bugfix $(RM) -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/models/$$i; done $(RM) src/network/scanwise_server # clean documentation $(RM) docs/temp.tex $(RM) docs/api.* $(RM) docs/wise2.image.tex $(RM) docs/*.pdf $(RM) docs/*.aux $(RM) docs/*.log $(RM) docs/*.toc $(RM) docs/*.pdf $(RM) docs/*.dvi $(RM) docs/*.ps $(RM) docs/*.4ct $(RM) docs/*.4tc $(RM) docs/*.css $(RM) docs/*.idv $(RM) docs/*.lg $(RM) docs/*.tmp $(RM) docs/*.xref $(RM) docs/*.haux $(RM) docs/*.htoc $(RM) docs/*.html $(RM) -r docs/api $(RM) -r docs/dynamite $(RM) -r docs/wise2 dh_clean override_dh_builddeb: dh_builddeb -- -Z xz debian/wise-doc.doc-base.wise0000644000000000000000000000047210771072112013246 0ustar Document: wise Title: Debian wise2 Manual Author: Ewan Birney, Richard Copley Abstract: This manual describes wise program usages. Section: Science/Biology Format: PDF Files: /usr/share/doc/wise-doc/wise2.pdf.gz Format: HTML Index: /usr/share/doc/wise-doc/wise2/wise2.html Files: /usr/share/doc/wise-doc/wise2/* debian/manpages0000644000000000000000000000053210673424515010713 0ustar debian/manpages.d/dba.1 debian/manpages.d/dnal.1 debian/manpages.d/estwise.1 debian/manpages.d/estwisedb.1 debian/manpages.d/genewise.1 debian/manpages.d/genewisedb.1 debian/manpages.d/genomewise.1 debian/manpages.d/promoterwise.1 debian/manpages.d/psw.1 debian/manpages.d/pswdb.1 debian/manpages.d/scanwise.1 debian/manpages.d/scanwise_server.1 debian/upstream0000644000000000000000000000105311754175070010757 0ustar Homepage: http://www.ebi.ac.uk/~birney/wise2/ Name: Wise2 Watch: | version=3 http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \ debian uupdate Webservice: http://www.ebi.ac.uk/Tools/Wise2/ Reference: Author: Ewan Birney and Michele Clamp and Richard Durbin Title: GeneWise and Genomewise Journal: Genome Research Year: 2004 Volume: 14 Number: 5 Pages: 988-95 DOI: 10.1101/gr.1865504 PMID: 15123596 URL: http://genome.cshlp.org/content/14/5/988.abstract eprint: http://genome.cshlp.org/content/14/5/988.full.pdf+html debian/docs0000644000000000000000000000000710673424515010045 0ustar README debian/source/0000755000000000000000000000000012171023446010466 5ustar debian/source/format0000644000000000000000000000001412101302227011662 0ustar 3.0 (quilt) debian/wise.install0000644000000000000000000000007412171023410011515 0ustar src/bin/* usr/bin src/models/genomewise usr/bin debian/wise-data.dirs0000644000000000000000000000001712166304007011724 0ustar usr/share/wise debian/copyright0000644000000000000000000001017311735302722011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz Files: * Copyright: © 1996-2001 Genome Research Limited (GRL) and Ewan Birney and Sean Eddy License: GRL All of the documentation and software included in the dyc directory of the Wise2 package directory is copyrighted by Genome Research Limited (GRL) and other individuals where appropriate. This license is modelled after the 'BSD' style license and is appropriate for use by both academic and commercial sites, without placing any restriction on the distribution of source code from other sources with this software. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1.Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2.Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3.Neither the name GRL nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . It is considered polite to indicate where appropriate that software which is developed using this source code includes a statement that it was developed using the Wise2 soure code. This is not a requirement however. . THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/HMMer2/* Copyright: © 1992-1996 Sean R. Eddy License: GPL-2 This source code is distributed under the terms of the GNU General Public License. See the files COPYING and GNULICENSE for details. Files: src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod src/dynlibsrc/histogram.tex Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy License: LGPL-any Converted by Ewan Birney to Dynamite source June 98. Copyright is LGPL. For more info read READMEs Comment: On Debian GNU/Linux systems, the complete text of the GNU Lesser General Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. Files: debian/* Copyright: © 2006-2007 Philipp Benner © 2009 Steffen Moeller © 2009 Charles Plessy © 2009 Barry deFreese License: GPL-2+ 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. Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL-3'. debian/control0000644000000000000000000000544212166304007010575 0ustar Source: wise Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Philipp Benner , Steffen Moeller , Charles Plessy Build-Depends: debhelper (>= 8), dpkg-dev (>= 1.16.1~), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/ Homepage: http://www.ebi.ac.uk/~birney/wise2/ Package: wise Architecture: any Pre-Depends: dpkg (>= 1.15.6~) Depends: ${shlibs:Depends}, ${misc:Depends}, wise-data (= ${source:Version}) Suggests: wise-doc (= ${source:Version}) Description: comparison of biopolymers, commonly DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. Package: wise-doc Architecture: all Section: doc Pre-Depends: dpkg (>= 1.15.6~) Depends: ${misc:Depends} Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer Description: documentation for the wise package This package contains the documentation for Wise2, a package focused on comparisons of biopolymers, commonly DNA and protein sequences. Package: wise-data Architecture: all Section: doc Pre-Depends: dpkg (>= 1.15.6~) Depends: ${misc:Depends} Recommends: wise (= ${source:Version}) Description: data files for the wise package This package contains data files for Wise2, a package focused on comparisons of biopolymers, commonly DNA and protein sequences. debian/compat0000644000000000000000000000000211634070456010372 0ustar 8 debian/patches/0000755000000000000000000000000012171023446010615 5ustar debian/patches/series0000644000000000000000000000024412166251154012035 0ustar 01_welcome-csh.patch 02_isnumber.patch 03_doc-nodycache.patch 04_wise2-pdflatex-update.patch 05_glib2.patch 06_getline.patch 07_ld--as-needed.patch 08_mayhem.patch debian/patches/07_ld--as-needed.patch0000644000000000000000000000716312101302227014440 0ustar Description: Fix FTBFS with ld --as-needed. Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 diff --git a/src/models/makefile b/src/models/makefile index 1766fee..e4634b5 100644 --- a/src/models/makefile +++ b/src/models/makefile @@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) scanwisep_compress.o : scanwisep.c $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c @@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) genewise : genewise.o $(NEWG) - $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) cdnawise : cdnawise.o $(NEWG) cdnawise10.o $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) @@ -300,16 +300,16 @@ efgw : genewise.o $(NEWG) genewisedb : genewisedb.o $(NEWG) - $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) estwisedb : estwisedb.o $(NEWG) - $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) edb : estwisedb.o $(NEWG) $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence estwise : estwise.o $(NEWG) - $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o @@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) pseudowise : pseudowise.o pseudowise7.o $(NEWG) - $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) debian/patches/03_doc-nodycache.patch0000755000000000000000000000156411137171477014662 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 03_doc-nodycache.dpatch by Philipp Benner ## ## DP: Documentation bugfix. @DPATCH@ diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex --- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100 +++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200 @@ -1617,7 +1617,8 @@ \item[-hithelp] more detailed help on hitlist formats \item[-dymem] memory style [default/linear/explicit] \item[-kbyte] memory amount to use [4000] -\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) +\item[-dycache] implicitly cache dy matrix usage (default) +\item[-nodycache] do not implicitly cache dy matrix usage \item[-dydebug] drop into dynamite dp matrix debugger \item[-paldebug] print PackAln after debugger run if used \item[-help] show help options debian/patches/02_isnumber.patch0000755000000000000000000000117611137171477014004 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 02_isnumber.dpatch by Philipp Benner ## ## DP: Replace isnumber() (which does not exist on linux) by isdigit(). @DPATCH@ diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c --- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200 +++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200 @@ -20,7 +20,7 @@ if( line[0] == '#' ) { continue; } - if( !isnumber(line[0]) ) { + if( !isdigit(line[0]) ) { warn("Bad looking line in intron file, %s",line); continue; } debian/patches/01_welcome-csh.patch0000755000000000000000000000200011137171477014350 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 01_welcome-csh.dpatch by Philipp Benner ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: No description. @DPATCH@ diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile --- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200 +++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200 @@ -109,7 +109,7 @@ bin : mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin - csh welcome.csh + ./welcome.csh libs : (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh --- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200 +++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/tcsh -f +#!/bin/sh echo "" echo "Welcome to Wise2.4" debian/patches/08_mayhem.patch0000644000000000000000000000467112166257630013445 0ustar --- a/src/models/dbac.c +++ b/src/models/dbac.c @@ -535,8 +535,12 @@ * */ - one = read_fasta_file_Sequence(*argv++); - two = read_fasta_file_Sequence(*argv++); + if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { + fatal("Unable to read the sequence in file"); + } + if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { + fatal("Unable to read the sequence in file"); + } uppercase_Sequence(one); uppercase_Sequence(two); --- a/src/models/estwise.c +++ b/src/models/estwise.c @@ -313,7 +313,7 @@ } } - if( reverse == TRUE ) { + if( cdna && reverse == TRUE ) { if( tstart > tend ) { warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); } @@ -323,7 +323,7 @@ cdna = cdna_temp; } - if( target_abs == TRUE ) { + if( cdna && target_abs == TRUE ) { cdna->baseseq->offset = 1; cdna->baseseq->end = strlen(cdna->baseseq->seq); } @@ -472,8 +472,11 @@ } cp = flat_cDNAParser(indel_error); - cm = flat_CodonMapper(ct); - sprinkle_errors_over_CodonMapper(cm,subs_error); + + if( ct ) { + cm = flat_CodonMapper(ct); + sprinkle_errors_over_CodonMapper(cm,subs_error); + } return ret; --- a/src/models/genewise.c +++ b/src/models/genewise.c @@ -550,8 +550,10 @@ ret = FALSE; } - gen->baseseq->offset = 1; - gen->baseseq->end = strlen(gen->baseseq->seq); + if ( gen ) { + gen->baseseq->offset = 1; + gen->baseseq->end = strlen(gen->baseseq->seq); + } } if( alg_str != NULL ) { --- a/src/models/estwisedb.c +++ b/src/models/estwisedb.c @@ -688,8 +688,11 @@ cps = flat_cDNAParser(indel_error); - cm = flat_CodonMapper(ct); - sprinkle_errors_over_CodonMapper(cm,subs_error); + + if( ct ) { + cm = flat_CodonMapper(ct); + sprinkle_errors_over_CodonMapper(cm,subs_error); + } return ret; --- a/src/models/promoterwise.c +++ b/src/models/promoterwise.c @@ -147,8 +147,12 @@ lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); - query = read_fasta_file_Sequence(argv[1]); - target = read_fasta_file_Sequence(argv[2]); + if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { + fatal("Unable to read the sequence in query file"); + } + if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { + fatal("Unable to read the sequence in target file"); + } for(i=0;ilen;i++) { query->seq[i] = toupper(query->seq[i]); debian/patches/06_getline.patch0000644000000000000000000001565011273126456013610 0ustar Index: wise-2.4.1/src/HMMer2/sqio.c =================================================================== --- wise-2.4.1.orig/src/HMMer2/sqio.c 2009-10-31 20:10:25.000000000 +0000 +++ wise-2.4.1/src/HMMer2/sqio.c 2009-10-31 20:11:11.000000000 +0000 @@ -213,7 +213,7 @@ } } -/* Function: getline() +/* Function: getline_() * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] * * Purpose: read a line from a sequence file into V->sbuffer. @@ -229,7 +229,7 @@ * Returns: (void) */ static void -getline(struct ReadSeqVars *V) +getline_(struct ReadSeqVars *V) { char *cp; @@ -299,7 +299,7 @@ V->seqlen = 0; if (addfirst) addseq(V->sbuffer, V); do { - getline(V); + getline_(V); /* feof() alone is a bug; files not necessarily \n terminated */ if (*(V->sbuffer) == '\0' && feof(V->f)) done = TRUE; @@ -327,7 +327,7 @@ char *sptr; /* load first line of entry */ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) - getline(V); + getline_(V); if (feof(V->f)) return; if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) @@ -336,7 +336,7 @@ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { - getline(V); + getline_(V); if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) @@ -345,7 +345,7 @@ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); - getline(V); /* skip next line, coords */ + getline_(V); /* skip next line, coords */ readLoop(0, endPIR, V); @@ -359,7 +359,7 @@ /* get next line */ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) - getline(V); + getline_(V); } @@ -377,7 +377,7 @@ char *nm; /* position past ';' comments */ do { - getline(V); + getline_(V); } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); if (!feof(V->f)) @@ -389,7 +389,7 @@ } while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) - getline(V); + getline_(V); } static int @@ -411,7 +411,7 @@ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); } - getline(V); + getline_(V); } if (! feof(V->f)) @@ -420,7 +420,7 @@ /* load next line */ while ((!feof(V->f)) && (*V->sbuffer != ';')) - getline(V); + getline_(V); } @@ -438,7 +438,7 @@ int in_definition; while (strncmp(V->sbuffer, "LOCUS", 5) != 0) - getline(V); + getline_(V); if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) { @@ -449,7 +449,7 @@ in_definition = FALSE; while (! feof(V->f)) { - getline(V); + getline_(V); if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) { if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) @@ -482,11 +482,11 @@ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) - getline(V); + getline_(V); /* SRE: V->s now holds "//", so sequential reads are wedged: fixed Tue Jul 13 1993 */ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) - getline(V); + getline_(V); } static int @@ -515,7 +515,7 @@ Die("bogus GCGdata format? %s", V->sbuffer); /* second line contains free text description */ - getline(V); + getline_(V); SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); if (binary) { @@ -535,7 +535,7 @@ else readLoop(0, endGCGdata, V); while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) - getline(V); + getline_(V); } static int @@ -555,12 +555,12 @@ if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); /* workaround for long NCBI NR lines */ - while (V->longline && ! feof(V->f)) getline(V); + while (V->longline && ! feof(V->f)) getline_(V); readLoop(0, endPearson, V); while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) - getline(V); + getline_(V); } @@ -587,7 +587,7 @@ /* make sure we have first line */ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) - getline(V); + getline_(V); if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) { @@ -596,7 +596,7 @@ } do { - getline(V); + getline_(V); if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) { if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) @@ -620,7 +620,7 @@ /* load next record's ID line */ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) - getline(V); + getline_(V); } @@ -636,7 +636,7 @@ { char *sptr; - getline(V); /*s == "seqLen seqid string..."*/ + getline_(V); /*s == "seqLen seqid string..."*/ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); @@ -647,7 +647,7 @@ readLoop(0, endZuker, V); while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) - getline(V); + getline_(V); } static void @@ -669,7 +669,7 @@ do { done = feof(V->f); - getline(V); + getline_(V); if (! done) addseq(V->sbuffer, V); } while (!done); } @@ -681,7 +681,7 @@ char *sptr; int dostruc = FALSE; - while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); + while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); @@ -689,7 +689,7 @@ /*CONSTCOND*/ while (1) { - getline(V); + getline_(V); if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } if (strncmp(V->sbuffer, "SRC ", 4) == 0) @@ -721,14 +721,14 @@ while (1) { /* sequence line */ - getline(V); + getline_(V); if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) break; addseq(V->sbuffer, V); /* structure line */ if (dostruc) { - getline(V); + getline_(V); if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } addstruc(V->sbuffer, V); } @@ -736,7 +736,7 @@ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) - getline(V); + getline_(V); } @@ -816,7 +816,7 @@ /* Load the first line. */ - getline(dbfp); + getline_(dbfp); return dbfp; } @@ -833,7 +833,7 @@ Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); fseek(sqfp->f, offset, SEEK_SET); - getline(sqfp); + getline_(sqfp); } @@ -853,7 +853,7 @@ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; else { rewind(sqfp->f); - getline(sqfp); + getline_(sqfp); } } @@ -949,7 +949,7 @@ do { /* skip leading comments on GCG file */ gotuw = (strstr(V->sbuffer,"..") != NULL); if (gotuw) readUWGCG(V); - getline(V); + getline_(V); } while (! feof(V->f)); break; debian/patches/04_wise2-pdflatex-update.patch0000755000000000000000000000222411137171477016273 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 04_wise2-pdflatex-update.dpatch by Philipp Benner ## ## DP: Make wise2.tex pdflatex compatible. @DPATCH@ diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex --- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200 +++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200 @@ -1,6 +1,7 @@ \documentclass{article} -\usepackage{epsfig} +%\usepackage{epsfig} +\usepackage{graphicx} \begin{document} \newcommand{\programtext}[1]{{\tt #1}} @@ -707,8 +708,9 @@ \begin{figure} \begin{center} \leavevmode -\epsfxsize 300pt -\epsfbox{genewise21.eps} +%\epsfxsize 300pt +%\epsfbox{genewise21.eps} +%\includegraphics[scale=0.75]{genewise21.pdf} \newline \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the arrows between them transitions. Black transitions are standard @@ -898,8 +900,9 @@ \begin{figure} \begin{center} \leavevmode -\epsfxsize 300pt -\epsfbox{genewise6.eps} +%\epsfxsize 300pt +%\epsfbox{genewise6.eps} +%\includegraphics[scale=0.75]{genewise6.pdf} \newline \caption{GeneWise6:23} \label{Figure:genewise623} debian/patches/05_glib2.patch0000644000000000000000000014105312166252351013150 0ustar Author: Barry deFreese Description: To build wise2 with the Glib version 2.0 instead of 1.2. Forwarded: birney@sanger.ac.uk --- a/src/makefile +++ b/src/makefile @@ -31,13 +31,13 @@ # Intel icc flags -# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` +# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` # alpha flags (-pthread) -# CFLAGS = -c -O3 -pthread `glib-config --cflags` +# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` # normal linux/bsd/mac flags -CFLAGS = -c -O3 `glib-config --cflags` +CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` EXTRALIBS = -lm --- a/src/snp/makefile +++ b/src/snp/makefile @@ -5,9 +5,9 @@ CC = cc #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. -CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm +LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm AR_OPTIONS = ru RANLIB_NEEDED = 0 @@ -16,7 +16,7 @@ $(CC) $(CFLAGS) $(INCFLAGS) $? test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o - $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) + $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) INCFLAGS = -I../base/ -I../dynlibsrc/ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn --- a/src/corba/makefile +++ b/src/corba/makefile @@ -3,9 +3,9 @@ CC = cc INCFLAGS = -I../base/ -I../dynlibsrc #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ -#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ -CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` -LFLAGS = -L../base/ -lm -lpthread +#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ +CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +LDFLAGS += -L../base/ -lm -lpthread AR_OPTIONS = ru @@ -14,18 +14,18 @@ orbit-idl hspscan_corba.idl test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o - cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o - cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o - cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o - cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread .c.o : $(CC) $(CFLAGS) $(INCFLAGS) $? --- a/src/models/makefile +++ b/src/models/makefile @@ -62,46 +62,46 @@ # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c testgenestat : testgenestat.o genestats.o pwmdna.o - $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) test_aligng : test_aligng.o aligngenemodel.o pwmdna.o - $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) makepwm : makepwm.o pwmdna.o - $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) testwise2xhmmer2.o : testwise2xhmmer2.c $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o - $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) + $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) plan7test.o : plan7test.c $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o - $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) + $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) seqstat : seqstat.o - $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) mutatedna : mutatedna.o - $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) revcomp : revcomp.o - $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) stupid_motif_scan : stupid_motif_scan.o - $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) seqtrunc : seqtrunc.o - $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) seqlist : seqlist.o - $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) testpwm : testpwm.o pwmdna.o - $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence + $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence threestate : $(MODELOBJ) @@ -111,29 +111,29 @@ pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o test : test.o proteinsw.o protprotdis.o - $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) + $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o - $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) test_tf : test_transfactor.o transfactor.o pwmdna.o - $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o - $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o - $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o - $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase cdtest : cdtest.o cdna2genomic.o d2d_display.o - $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) + $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) prob2bits : prob2bits.o - $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase + $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase quick : cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c @@ -180,161 +180,161 @@ $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. oldpostwise : oldpostwise.o $(NEWG) - $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase + $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase testdna : testdna.o dnaalign.o seqaligndisplay.o - $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) dnal : dnal.o dnaalign.o seqaligndisplay.o - $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o - $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) scanwisep.o : scanwisep.c - $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? + $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? hsp2aln_sw.o : hsp2aln_sw.c - $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? + $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? scanwisep_mysql.o : scanwisep.c $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ + $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ scanwisep_corba.o : scanwisep.c $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread + $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread scanwisep_wiseserver.o : scanwisep.c $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread scanwisep_compress.o : scanwisep.c $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o - $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread + $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread test_gwhsp : test_gwhsp.o genewisehsp.o - $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread + $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread localcishit.o : localcishit.c - $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? + $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? promoterwise.o : promoterwise.c - $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? + $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o - $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread + $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o - $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread + $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o - $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread + $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o - $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o - $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o - $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) + $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o - $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) lba : lba.o largeblockdp.o seqaligndisplay.o - $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o - $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o - $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o - $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) makerandomdb : makerandomdb.o - $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) genewise : genewise.o $(NEWG) - $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) cdnawise : cdnawise.o $(NEWG) cdnawise10.o - $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o - $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o - $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o - $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o - $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase + $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase efgw : genewise.o $(NEWG) - $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence genewisedb : genewisedb.o $(NEWG) - $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) estwisedb : estwisedb.o $(NEWG) - $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) edb : estwisedb.o $(NEWG) - $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence estwise : estwise.o $(NEWG) - $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o - $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o - $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o - $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o - $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o - $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o - $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) pseudowise : pseudowise.o pseudowise7.o $(NEWG) - $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o - $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) HMMER_LIBS = ../HMMer2/ @@ -345,11 +345,11 @@ CC = cc #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. -CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` -#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` -#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ +CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` +#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` +#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ -LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` +LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` AR_OPTIONS = ru RANLIB_NEEDED = 0 @@ -360,7 +360,7 @@ #test : test.o libwisedb.a -# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) +# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) # --- a/src/dnaindex/makefile +++ b/src/dnaindex/makefile @@ -27,53 +27,53 @@ kwise : kwise.o $(ASSEMBLY_OBJ) - $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` + $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) - $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` + $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) - $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` + $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` make_shotgun : make_shotgun.o shotgun.o - $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) test_dnanumber : test_dnanumber.o dnanumber.o - $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) test_linkindex : test_linkindex.o linkindex.o dnanumber.o - $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) test_forwardindex : test_forwardindex.o forwardindex.o - $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) test_euler : test_euler.o eulerindex.o singleseqspace.o - $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o - $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o - $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o - $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o - $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) show_euler : show_euler.o eulerindex.o singleseqspace.o - $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) CC = cc -CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` +CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm +LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm .c.o : --- a/src/dnaindex/assembly/makefile +++ b/src/dnaindex/assembly/makefile @@ -3,33 +3,33 @@ .SUFFIXES : .dy test_basegraph : test_basegraph.o basegraph.o - $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o - $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o - $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o - $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o - $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o - $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase + $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase CC = cc -CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` +CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm +LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm .c.o : --- a/src/dynlibsrc/makefile +++ b/src/dynlibsrc/makefile @@ -84,11 +84,11 @@ CC = cc INCFLAGS = -I../base/ #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ -CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` -#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` -#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` +CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ -LFLAGS = -g -L../base/ -lm +LDFLAGS += -g -L../base/ -lm AR_OPTIONS = ru RANLIB_NEEDED = 0 @@ -133,47 +133,47 @@ # test_genomic : genomic.o test_genomic.o sequence.o codon.o - $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm test_tree : tree.o test_tree.o - $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm test_intallocator : intallocator.o test_intallocator.o - $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm test_psi : test_psi.o proteinstreamedindex.o - $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a - $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a - $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o - $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` + $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o - $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` + $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o - $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm testseqalign : seqalign.o testseqalign.o sequence.o codon.o - $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm testanc : libdyna.a - $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm testdb : testdb.o sequencedb.o sequence.o codon.o probability.o - $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o - $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o - $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm .c.o : $(CC) $(CFLAGS) $(INCFLAGS) $? --- a/src/network/makefile +++ b/src/network/makefile @@ -3,8 +3,8 @@ CC = cc INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex -CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` -LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` +CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` +LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` AR_OPTIONS = ru RANLIB_NEEDED = 0 @@ -13,7 +13,7 @@ scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o - $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread + $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread .c.o : --- a/src/other_programs/makefile +++ b/src/other_programs/makefile @@ -3,8 +3,8 @@ .SUFFIXES : .dy CC = cc -CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` -LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` +CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` +LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` AR_OPTIONS = ru RANLIB_NEEDED = 0 --- a/src/base/makefile +++ b/src/base/makefile @@ -19,9 +19,9 @@ -#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH -CFLAGS = -c -O2 -DUNIX -pthread -LFLAGS = -g -lm +#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH +CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread +LDFLAGS += -g -lm DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D AR_OPTIONS = ru --- a/src/HMMer2/Makefile +++ b/src/HMMer2/Makefile @@ -13,7 +13,7 @@ ## your compiler and compiler flags # CC = cc -CFLAGS = -g +CFLAGS += $(CPPFLAGS) -g ## machine specific definitions # @@ -75,25 +75,25 @@ all: $(PROGS) hmmalign: $(OBJ) hmmalign.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) hmmbuild: $(OBJ) hmmbuild.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) hmmcalibrate: $(OBJ) hmmcalibrate.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) hmmconvert: $(OBJ) hmmconvert.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) hmmemit: $(OBJ) hmmemit.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) hmmpfam: $(OBJ) hmmpfam.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) hmmsearch: $(OBJ) hmmsearch.o - $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) ####### ## Target used in making Shiva test suite debian/changelog0000644000000000000000000001401612171020734011037 0ustar wise (2.4.1-14) unstable; urgency=low * Fixed FTBFS bug (Closes: #716983). -- Philipp Benner Mon, 15 Jul 2013 18:22:15 +0200 wise (2.4.1-13) unstable; urgency=low * Added mayhem bugfixes. * Moved examples/ from wise-doc to wise-data package. * Removed -O3 cflag from makefiles. -- Philipp Benner Sun, 07 Jul 2013 13:33:01 +0200 wise (2.4.1-12) unstable; urgency=low * Added missing -D_FORTIFY_SOURCE=2 for hardening support * Standards version 3.9.4 -- Philipp Benner Mon, 28 Jan 2013 20:33:16 +0100 wise (2.4.1-11) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add publication data [ Philipp Benner ] * Added hardening flags -- Philipp Benner Sun, 27 Jan 2013 18:05:31 +0100 wise (2.4.1-10) unstable; urgency=low * Convert debian/rules to dh, Closes: #666319, as it restores build flags. * Verbose debhelper in debian/rules. * Normalised and upgraded debian/copyright file with ‘cme fix’. * Pre-Depends on dpkg (>= 1.15.6~) (debian/control). * Conforms to Debian policy 3.9.3 (debian/control, no other changes needed). * Convert debian/rules to dh, Closes: #666319, as it restores build flags. * Documented metadata in debian/upstream. -- Charles Plessy Fri, 30 Mar 2012 19:25:53 +0900 wise (2.4.1-9) unstable; urgency=low * Correct src/models/makefile to link --as-needed (Closes: #641333). * Conforms with Policy 3.9.2 (debian/control, no other changes needed). * Corrected VCS URLs (debian/control). * Use Debhelper 8 (debian/compat, debian/control). * Added build-arch and build-indep targets to debian/rules. * Machine-readable debian/copryight file conforms to DEP 5. * Compress binary package with xz (debian/rules). -- Charles Plessy Wed, 14 Sep 2011 17:52:32 +0900 wise (2.4.1-8) unstable; urgency=low * Fixed conflicting definitions of getline(). (Closes: #552821) * Added README.source. * Standards version 3.8.3. * Fixed spelling error in package description. -- Philipp Benner Sat, 31 Oct 2009 21:25:52 +0000 wise (2.4.1-7) unstable; urgency=low [ Steffen Moeller ] * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese. * Updated policy to 3.8.1 (no changes required). * fixed api->API lintian warning. [ Charles Plessy ] * debian/control: - Added myself to the Uploaders. - Added ${misc:Depends} to the package dependencies. - Using Debhelper 7 (also debian/compat). - Eliminated redundancy between the long descriptions of wise and wise-doc. * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules. -- Charles Plessy Mon, 15 Jun 2009 20:49:27 +0900 wise (2.4.1-6) unstable; urgency=low * Updated policy to 3.8.0 (no changes required). * wise now suggests wise-doc (downgraded from 'recommends'). [ Steffen Moeller ] * Using quilt instead of dpatch. [ Philipp Benner ] -- Philipp Benner Sun, 25 Jan 2009 22:57:27 +0000 wise (2.4.1-5) unstable; urgency=low * Removed a bashism in debian/rules (Closes: #478639). -- Charles Plessy Sun, 04 May 2008 15:19:01 +0900 wise (2.4.1-4) unstable; urgency=low * Changed the doc-base section according to the new policy [Charles Plessy]. -- Philipp Benner Mon, 31 Mar 2008 10:07:35 +0200 wise (2.4.1-3) unstable; urgency=low * New maintainer e-mail address. * debian/control: Added DM-Upload-Allowed: yes. -- Philipp Benner Mon, 14 Jan 2008 18:33:27 +0100 wise (2.4.1-2) unstable; urgency=low * Using official Vcs-Browser and Vcs-Svn fields (debian/control). * Moved the Homepage: field out from the package's description + (Charles Plessy). * Converted copyright file to machine interpretable format. * Changed maintainer to Debian-Med Packaging Team. -- Philipp Benner Sun, 02 Dec 2007 16:15:50 +0100 wise (2.4.1-1) unstable; urgency=low * New upstream release. -- Philipp Benner Sat, 15 Sep 2007 17:18:49 +0200 wise (2.4.0-3) unstable; urgency=low * Removed debtags from debian/control. * Updated package description (Closes: #435904). * Excluded genewise21.eps and genewise6.eps from documentation + (workaround for a bug in gs-esp). -- Philipp Benner Sun, 05 Aug 2007 20:21:35 +0200 wise (2.4.0-2) unstable; urgency=low * Converted wise2.tex to a pdflatex compatible latex file + (workaround for a bug in dvips) -- Philipp Benner Fri, 27 Jul 2007 18:46:33 +0200 wise (2.4.0-1) unstable; urgency=low * New upstream release (Closes: #431392) * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit() * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix -- Philipp Benner Tue, 24 Jul 2007 11:58:36 +0200 wise (2.2.0-5) unstable; urgency=low * Removed obsolete dependencies (Closes: #422123) -- Philipp Benner Sun, 6 May 2007 22:42:27 +0200 wise (2.2.0-4) unstable; urgency=low * Adapted debian-med tags * Uscan support * Migrating to texlive * use /bin/sh instead of /bin/csh in src/welcome.csh -- Philipp Benner Tue, 27 Mar 2007 19:29:08 +0200 wise (2.2.0-3) unstable; urgency=low * package tags * fixed typos in package description -- Philipp Benner Thu, 21 Sep 2006 14:22:39 +0200 wise (2.2.0-2) unstable; urgency=low * removed \ref tags from package description * moved examples to package wise-doc * fixed typo in README.Debian * minor changes in debian/control * fixed typo in package description (Closes: #380451) * new html documentation -- Philipp Benner Sun, 30 Jul 2006 14:08:20 +0200 wise (2.2.0-1) unstable; urgency=low * Initial release (Closes: #379604) -- Philipp Benner Sun, 23 Jul 2006 17:29:49 +0200 debian/manpages.d/0000755000000000000000000000000012171023446011203 5ustar debian/manpages.d/estwise.sgml0000644000000000000000000000775510673424515013577 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> ESTWISE"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; comparison of a related protein to cDNA (or ESTs) &dhpackage; options protein-file dna-file DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/pswdb.sgml0000644000000000000000000000772610673424515013231 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> PSWDB"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; protein smith waterman database &dhpackage; options query_db target_db DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/scanwise.sgml0000644000000000000000000000774310724565070013724 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> SCANWISE"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2007 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; Fast but sensitive search method for biopolymers &dhpackage; options query_sequence_file_fasta DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/genomewise.sgml0000644000000000000000000000777110724565070014253 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> GENOMEWISE"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; A tool for combining disparate evidence strands &dhpackage; options genomic-fasta-file evidence-file DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/genewise.sgml0000644000000000000000000000775310673424515013720 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> GENEWISE"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; comparison of a related protein to genomic DNA &dhpackage; options protein-file dna-file DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/Makefile0000644000000000000000000000041410673424515012651 0ustar SHELL = /bin/sh MANPAGES = dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 all: $(MANPAGES) $(MANPAGES): %.1 : %.sgml docbook-to-man $< > $@ clean: $(RM) $(MANPAGES) .PHONY: all debian/manpages.d/dnal.sgml0000644000000000000000000000767010673424515013026 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> DNAL"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; ... &dhpackage; options dna-file dna-file DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/dba.sgml0000644000000000000000000001114310673424515012624 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> DBA"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; characterising shared regulatory regions of genomic DNA &dhpackage; options seq1 seq2 DESCRIPTION dba - standing for Dna Block Aligner, was developped by Niclas Jareborg, Richard Durbin and Ewan Birney for characterising shared regulatory regions of genomic DNA, either in upstream regions or introns of genes The idea was that in these regions there would a series of shared motifs, perhaps with one or two insertions or deletions but between motifs there would be any length of sequence. The subsquent model was a 3 state model which was log-odd'd ratio to a null model of their being no examples of a motif in the two sequences. OPTIONS Show summary of options. Show version of program. SEE ALSO dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/promoterwise.sgml0000644000000000000000000000774310673424515014650 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> PROMOTERWISE"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2007 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; comparison between two promoter sequences &dhpackage; options query_sequence target_sequence DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), psw (1), pswdb (1) scanwise (1) scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/estwisedb.sgml0000644000000000000000000000777210673424515014104 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> ESTWISEDB"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; a database of proteins vs a database of EST/cDNA sequences &dhpackage; options protein-input dna-input DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/scanwise_server.sgml0000644000000000000000000000773410724565070015312 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> SCANWISE_SERVER"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; Server for scanwise &dhpackage; options sequence_file_fasta DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/genewisedb.sgml0000644000000000000000000000777410673424515014231 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> GENEWISEDB"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; a database of proteins vs a database of genomic dna sequences &dhpackage; options protein-input dna-input DESCRIPTION not available OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/manpages.d/psw.sgml0000644000000000000000000001025010673424515012705 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Philipp"> Benner"> July 2006"> 1"> mail@philipp-benner.de"> PSW"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2006 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; Protein Smith-Waterman and other comparisons &dhpackage; options seq1 seq2 DESCRIPTION psw is a short and sweet program for calculating smith waterman alginments quickly. It was mainly written as C driver to test the underlying code which is more useful in things like the Perl port. OPTIONS Show summary of options. Show version of program. SEE ALSO dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), pswdb (1), scanwise (1), scanwise_server (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/wise-doc.docs0000644000000000000000000000012010673424515011552 0ustar docs/api.pdf docs/dynamite.pdf docs/wise2.pdf docs/api docs/dynamite docs/wise2 debian/wise-data.install0000644000000000000000000000003112171023425012423 0ustar wisecfg/* usr/share/wise debian/README.source0000644000000000000000000000064011273126456011354 0ustar 01_welcome-csh.patch: Removes dependencies on csh and tcsh. 02_isnumber.patch: Replaces isnumber() with isdigit(). 03_doc-nodycache.patch: Bugfix in documentation. 04_wise2-pdflatex-update.patch: Use pdflatex instead of latex. 05_glib2.patch: Use glib2 instead of glib1. 06_getline.patch: Fixes conflicting definitions of getline. -- Philipp Benner , Sat, 31 Oct 2009 21:12:15 +0000 debian/watch0000644000000000000000000000013310724554313010220 0ustar version=3 http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \ debian uupdate debian/wise-doc.doc-base.dynamite0000644000000000000000000000055310771072112014111 0ustar Document: wise-dynamite Title: Wise dynamite Manual Author: Ewan Birney Abstract: This manual describes the dynamite code generating language for dynamic programming. Section: Science/Biology Format: PDF Files: /usr/share/doc/wise-doc/dynamite.pdf.gz Format: HTML Index: /usr/share/doc/wise-doc/dynamite/dynamite.html Files: /usr/share/doc/wise-doc/dynamite/*