debian/0000755000000000000000000000000011735064015007170 5ustar debian/upstream0000644000000000000000000000107511735062754010766 0ustar Name: ProDA Homepage: http://proda.stanford.edu/ Reference: author: Phuong, Tu Minh and Do, Chuong B. and Edgar, Robert C. and Batzoglou, Serafim title: Multiple alignment of protein sequences with repeats and rearrangements journal: Nucl. Acids Res. volume: 34 number: 20 pages: 5932-5942 year: 2006 PMID: 17068081 DOI: 10.1093/nar/gkl511 URL: http://nar.oxfordjournals.org/cgi/content/abstract/34/20/5932 eprint: http://nar.oxfordjournals.org/cgi/reprint/34/20/5932.pdf Watch: | opts="uversionmangle=s/_/\./" \ http://proda.stanford.edu/proda_(.*)\.tar\.gz debian/source/0000755000000000000000000000000011735063270010472 5ustar debian/source/format0000644000000000000000000000001411606404406011675 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000202111110210220011070 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Upstream-Author: Phuong Tu Minh Do Chuong B. Edgar Robert C. Batzoglou Serafim Original-Source-Location: http://proda.stanford.edu/proda_1_0.tar.gz Packaged-By: David Paleino Packaged-Date: Tue, 24 Apr 2007 12:47:45 +0200 Files: * Copyright: © 2006, Phuong Tu Minh © 2006, Do Chuong B. © 2006, Edgar Robert C. © 2006, Batzoglou Serafim License: PD ProDA is released under public domain, it has been published in: Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research 2006 34(20), 5932-5942 - by Phuong T.M., Do C.B., Edgar R.C. and Batzoglou S. Files: debian/* Copyright: © 2007-2008, David Paleino © 2008 Charles Plessy License: Same as Proda itself debian/proda.1.xml0000644000000000000000000002415711110210220011141 0ustar .
will be generated. You may view the manual page with: nroff -man .
| less'. A typical entry in a Makefile or Makefile.am is: DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\ manpages/docbook.xsl XP=xsltproc -''-nonet manpage.1: manpage.dbk $(XP) $(DB2MAN) $< The xsltproc binary is found in the xsltproc package. The XSL files are in docbook-xsl. 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 xsltproc and docbook-xsl in your Build-Depends control field. --> David"> Paleino"> april 25, 2007"> 1"> d.paleino@gmail.com"> proda"> Debian"> GNU"> GPL"> ]>
&dhemail;
2007 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; multiple alignment of protein sequences with repeats and rearrangements &dhpackage; mfafile > output DESCRIPTION This manual page documents briefly the proda command. proda (Protein Domain Aligner) is public domain software for generating multiple alignments of protein sequences with repeats and rearrangements, e.g. proteins with multiple domains. Given a set of protein sequences as input, ProDA first finds local pairwise alignments between all pairs of sequences, then forms blocks of alignable sequence fragments, and finally generates multiple alignments of the blocks. ProDA relies on many techniques used in probcons (<http://probcons.stanford.edu>), a recent multiple aligner that shows high accuracy in a number of popular benchmarks. INPUT FORMAT Proda accepts input files in the MFA format. The MFA format is specified below: the MFA format consists of multiple sequences; each sequence in the MFA format begins with a single-line description, followed by lines of sequence data; the description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. OUTPUT FORMAT For a set of input sequences, Proda usually outputs several blocks in turn, each consists of alignable sequence fragments. Each block is followed by its multiple alignment. A block is specified by listing its sequence fragments. Each fragment is output as sequence_name(start-end), where sequence_name is the name of the original sequence and start and end are positions at which the fragment begins and ends respectively. Proda produces block alignments in the ClustalW (ALN) format described below: the ClustalW format consists of a single header line followed by sequence data in blocks of 50 alignment positions; each block consists of: one line of data for each of the sequences in the alignment - in particular, the name of the sequence; 50 characters of the alignment; one annotation line indicating fully conserved (*), strongly-conserved (:), or weakly-conserved columns (.); the description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. FASTA format for output If the -fasta option is specified, then, in addition to regular output, ProDA produces a file containing block alignments in the FASTA format. The output file has the same name as the first input file and extension ".fasta". Two consecutive block alignments are separated by a line containing character '#'. The FASTA format is described below: the FASTA format consists of all the sequences given in the input files; each sequence in the FASTA format begins with a single-line description, followed by lines of sequence data; the description line is distinguished from the sequence data by a greater-than (">") symbol in the first column; aligned residues are in upper case, unaligned residues are in lower case. Since a final alignment contains each sequence only once, this option should be used only if input sequences do not contain repeats. OPTIONS [min_length] Set minimal alignment length equal to [min_length]. ProDA finds alignments of length greater than or equal to a threshold L. By default, L = 30. This option sets the threshold to [min_length]. Use posterior decoding when computing local pairwise alignments. ProDA computes local pairwise alignments between two sequences using a pair-HMM and either Viterbi decoding or posterior decoding. The default option is using Viterbi decoding which is faster than posterior decoding but may be less accurate. Turning on this option instructs the aligner to use posterior decoding instead. In the example above, the output was generated with -posterior option turned on. Do not report progress while aligning. Turning on this option instructs the aligner not to report the progress while aligning. By default, ProDA reports the progress on all pairwise alignments, block generation, and on block alignment. Since some stages of the algorithm, especially pairwise alignment, may take long time, reporting progress makes the program look alive while running. Use transitivity when forming blocks of alignable sequence fragments. Two sequence fragments are directly alignable if they are parts of a local pairwise alignment. By default, two fragments are considered alignable if and only if they are directly alignable. Turning on this option instructs the aligner to consider two fragments alignable when they are directly alignable or when both of them are directly alignable to a third fragment. Use FASTA output format in addition to the ClustalW format. When this option is turned on, the aligner generates output in the FASTA format and stores in a file with the same name as the first input file and extension ".fasta", in addition to the normal output to stdout. This option should be used only if input sequences do not contain repeats. SEE ALSO probcons (1) AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). This man page is released under the same conditions as the software, that is Public Domain. This software has been released in Public Domain by Phuong T.M., Do C.B., Edgar R.C. and Batzoglou S. in "Multiple alignment of protein sequences with repeats and rearrangements", Nucleic Acids Research 2006 - 34(20), 5932-5942 debian/compat0000644000000000000000000000000211735063136010371 0ustar 9 debian/proda.10000644000000000000000000001472111110210220010336 0ustar .\" Title: proda .\" Author: .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: april 25, 2007 .\" Manual: .\" Source: .\" .TH "PRODA" "1" "april 25, 2007" "" "" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" proda - multiple alignment of protein sequences with repeats and rearrangements .SH "SYNOPSIS" .HP 6 \fBproda\fR [\fB\fIoption\fR\fR] [\fImfafile\fR] [>\ \fIoutput\fR] .SH "DESCRIPTION" .PP This manual page documents briefly the \fBproda\fR command\. .PP \fBproda\fR (Protein Domain Aligner) is public domain software for generating multiple alignments of protein sequences with repeats and rearrangements, e\.g\. proteins with multiple domains\. .PP Given a set of protein sequences as input, ProDA first finds local pairwise alignments between all pairs of sequences, then forms blocks of alignable sequence fragments, and finally generates multiple alignments of the blocks\. ProDA relies on many techniques used in \fBprobcons\fR (), a recent multiple aligner that shows high accuracy in a number of popular benchmarks\. .SH "INPUT FORMAT" .PP Proda accepts input files in the MFA format\. The MFA format is specified below: .sp .RS 4 \h'-04'\(bu\h'+03'the MFA format consists of multiple sequences; .RE .sp .RS 4 \h'-04'\(bu\h'+03'each sequence in the MFA format begins with a single\-line description, followed by lines of sequence data; .RE .sp .RS 4 \h'-04'\(bu\h'+03'the description line is distinguished from the sequence data by a greater\-than (">") symbol in the first column\. .RE .SH "OUTPUT FORMAT" .PP For a set of input sequences, Proda usually outputs several blocks in turn, each consists of alignable sequence fragments\. Each block is followed by its multiple alignment\. .PP A block is specified by listing its sequence fragments\. Each fragment is output as sequence_name(start\-end), where sequence_name is the name of the original sequence and start and end are positions at which the fragment begins and ends respectively\. .PP Proda produces block alignments in the ClustalW (ALN) format described below: .sp .RS 4 \h'-04'\(bu\h'+03'the ClustalW format consists of a single header line followed by sequence data in blocks of 50 alignment positions; .RE .sp .RS 4 \h'-04'\(bu\h'+03'each block consists of: .sp .RS 4 \h'-04'\(bu\h'+03'one line of data for each of the sequences in the alignment \- in particular, the name of the sequence; .RE .sp .RS 4 \h'-04'\(bu\h'+03'50 characters of the alignment; .RE .sp .RS 4 \h'-04'\(bu\h'+03'one annotation line indicating fully conserved (*), strongly\-conserved (:), or weakly\-conserved columns (\.); .RE .RE .sp .RS 4 \h'-04'\(bu\h'+03'the description line is distinguished from the sequence data by a greater\-than (">") symbol in the first column\. .RE .SS "FASTA format for output" .PP If the \-fasta option is specified, then, in addition to regular output, ProDA produces a file containing block alignments in the FASTA format\. The output file has the same name as the first input file and extension "\.fasta"\. Two consecutive block alignments are separated by a line containing character \'#\'\. .PP The FASTA format is described below: .sp .RS 4 \h'-04'\(bu\h'+03'the FASTA format consists of all the sequences given in the input files; .RE .sp .RS 4 \h'-04'\(bu\h'+03'each sequence in the FASTA format begins with a single\-line description, followed by lines of sequence data; .RE .sp .RS 4 \h'-04'\(bu\h'+03'the description line is distinguished from the sequence data by a greater\-than (">") symbol in the first column; .RE .sp .RS 4 \h'-04'\(bu\h'+03'aligned residues are in upper case, unaligned residues are in lower case\. .RE .PP Since a final alignment contains each sequence only once, this option should be used only if input sequences do not contain repeats\. .SH "OPTIONS" .PP \fB\-L\fR [min_length] .RS 4 .PP .RS 4 .PP Set minimal alignment length equal to [min_length]\. .PP ProDA finds alignments of length greater than or equal to a threshold L\. By default, L = 30\. This option sets the threshold to [min_length]\. .RE .RE .PP \fB\-posterior\fR .RS 4 .PP .RS 4 .PP Use posterior decoding when computing local pairwise alignments\. .PP ProDA computes local pairwise alignments between two sequences using a pair\-HMM and either Viterbi decoding or posterior decoding\. The default option is using Viterbi decoding which is faster than posterior decoding but may be less accurate\. Turning on this option instructs the aligner to use posterior decoding instead\. In the example above, the output was generated with \-posterior option turned on\. .RE .RE .PP \fB\-silent\fR .RS 4 .PP .RS 4 .PP Do not report progress while aligning\. .PP Turning on this option instructs the aligner not to report the progress while aligning\. By default, ProDA reports the progress on all pairwise alignments, block generation, and on block alignment\. Since some stages of the algorithm, especially pairwise alignment, may take long time, reporting progress makes the program look alive while running\. .RE .RE .PP \fB\-tran\fR .RS 4 .PP .RS 4 .PP Use transitivity when forming blocks of alignable sequence fragments\. .PP Two sequence fragments are directly alignable if they are parts of a local pairwise alignment\. By default, two fragments are considered alignable if and only if they are directly alignable\. Turning on this option instructs the aligner to consider two fragments alignable when they are directly alignable or when both of them are directly alignable to a third fragment\. .RE .RE .PP \fB\-fasta\fR .RS 4 .PP .RS 4 .PP Use FASTA output format in addition to the ClustalW format\. .PP When this option is turned on, the aligner generates output in the FASTA format and stores in a file with the same name as the first input file and extension "\.fasta", in addition to the normal output to stdout\. This option should be used only if input sequences do not contain repeats\. .RE .RE .SH "SEE ALSO" .PP \fBprobcons\fR (1) .SH "AUTHOR" .PP This manual page was written by David Paleino for the Debian(TM) system (but may be used by others)\. This man page is released under the same conditions as the software, that is Public Domain\. .PP This software has been released in Public Domain by Phuong T\.M\., Do C\.B\., Edgar R\.C\. and Batzoglou S\. in "Multiple alignment of protein sequences with repeats and rearrangements", Nucleic Acids Research 2006 \- 34(20), 5932\-5942 .SH "COPYRIGHT" Copyright \(co 2007 David Paleino .br debian/install0000644000000000000000000000001611110210220010530 0ustar proda usr/bin debian/control0000644000000000000000000000166711735063147010612 0ustar Source: proda Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proda/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proda/trunk/ Homepage: http://proda.stanford.edu/ Package: proda Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: multiple alignment of protein sequences ProDA is a system for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures. Given an input set of unaligned sequences, ProDA identifies all homologous regions appearing in one or more sequences, and returns a collection of local multiple alignments for these regions. debian/patches/0000755000000000000000000000000011735063331010617 5ustar debian/patches/01-fix_gcc4.3_warnings.patch0000644000000000000000000000323011735063322015613 0ustar Authors: David Paleino Forwarded: Phuong Tu Minh , Do Chuong B. Description: Corrects deprecated conversion from string constant to ‘char*’. License: Use, modify, redistribute under the same terms as Proda iteslf. --- proda.orig/Assert.cc +++ proda/Assert.cc @@ -10,7 +10,7 @@ // Write out assertion error message ////////////////////////////////////////////////////////////////////// -int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg){ +int _ASSERT_FAILED (const char *filename, int line_number, const char *error_msg){ fprintf (stderr, "Assertion failed in file \"%s\", line %d: %s\n", filename, line_number, error_msg); abort(); --- proda.orig/Assert.h +++ proda/Assert.h @@ -7,7 +7,7 @@ #ifndef ASSERT_H #define ASSERT_H -int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg); +int _ASSERT_FAILED (const char *filename, int line_number, const char *error_msg); #ifdef NDEBUG #define ASSERT(test,error_msg) --- proda.orig/MultiSequence.cc +++ proda/MultiSequence.cc @@ -386,7 +386,7 @@ ////////////////////////////////////////////////////////////////////// const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { - static char *groups[47] = { + static const char *groups[47] = { // Identities "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", --- proda.orig/ProbModel.cc +++ proda/ProbModel.cc @@ -30,7 +30,7 @@ { 0, 0, 0, 0, 0, 0, 1 } }; -char *ALPHABET = "ARNDCQEGHILKMFPSTWYV"; +const char *ALPHABET = "ARNDCQEGHILKMFPSTWYV"; float INIT_A = 0.9860202074; debian/patches/series0000644000000000000000000000013611110210220012006 0ustar 01-fix_gcc4.3_warnings.patch 02-fix_CXXFLAGS.patch 03-fix_FTBFS_gcc4.3_missing_includes.patch debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch0000644000000000000000000000336511735063331020261 0ustar Authors: David Paleino Forwarded: Phuong Tu Minh , Do Chuong B. Description: Patch for compiling with g++-4.3. GCC 4.3 has a stricter requirements for the declaration of includes. Without this patch, ProDA would not build with g++4.3. License: Use, modify, redistribute under the same terms as Proda iteslf. --- proda.orig/AlignedFragment.cc +++ proda/AlignedFragment.cc @@ -2,6 +2,7 @@ // ////////////////////////////////////////////////////////////////////// +#include #include "AlignedFragment.h" #include "Assert.h" #include "Utilities.h" --- proda.orig/AlignedFragment.h +++ proda/AlignedFragment.h @@ -7,7 +7,9 @@ #ifndef ALIGNFRAGMENT_H #define ALIGNFRAGMENT_H +#include #include +#include class Fragment; class AlignedFragment; --- proda.orig/Block.cc +++ proda/Block.cc @@ -2,6 +2,7 @@ // ////////////////////////////////////////////////////////////////////// +#include #include "Block.h" #include "AlignedFragment.h" #include "Sequence.h" --- proda.orig/Main.cc +++ proda/Main.cc @@ -6,6 +6,7 @@ #include #include #include +#include #include "Assert.h" #include "MultiSequence.h" #include "ProbModel.h" --- proda.orig/PairAligner.cc +++ proda/PairAligner.cc @@ -4,6 +4,8 @@ // Implementation of PairAligner class //////////////////////////////////////////////////////////////////// +#include +#include #include "PairAligner.h" #include "Utilities.h" #include "LocalAlign.h" --- proda.orig/ProbModel.cc +++ proda/ProbModel.cc @@ -4,6 +4,7 @@ #include #include +#include #include "ProbModel.h" #include "Utilities.h" debian/patches/02-fix_CXXFLAGS.patch0000644000000000000000000000411711110210220014121 0ustar Authors: Charles Plessy Forwarded: Phuong Tu Minh , Do Chuong B. Description: Patch for stricter use of CXXFLAGS. CXXFLAGS is a "user variable" that can be overriden at compilation time. The Debian build system overrides CXXFLAGS, breaking ProDA's build system that relies on it to pass -DVERSION="\"1.00\"" to the compiler. This patch replaces OTHERFLAGS by CPPFLAGS. This makes sure that -DVERSION="\"1.00\"" is passed to the complier for proda as well as all the .o files (build by implicit rule), even if CXXFLAGS is overriden. More information on user variables can be found at http://www.gnu.org/software/libtool/manual/automake/User-Variables.html#User-Variables and http://www.gnu.org/prep/standards/standards.html#Command-Variables License: Use, modify, redistribute under the same terms as Proda iteslf. --- proda.orig/Makefile +++ proda/Makefile @@ -15,17 +15,17 @@ # c) RELEASE mode ################################################################################ -OTHERFLAGS = -DVERSION="\"1.00\"" +CPPFLAGS = -DVERSION="\"1.00\"" # debug mode -CXXFLAGS = -g -W -Wall -pedantic $(OTHERFLAGS) +CXXFLAGS = -g -W -Wall -pedantic # profile mode -#CXXFLAGS = -pg -W -Wall -pedantic $(OTHERFLAGS) +#CXXFLAGS = -pg -W -Wall -pedantic # release mode -#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG -funroll-loops ################################################################################ # 3) Dependencies @@ -38,7 +38,7 @@ all : $(TARGETS) proda : $(OBJECTS) - $(CXX) $(CXXFLAGS) -lm $(OBJECTS) -o proda + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -lm $(OBJECTS) -o proda Assert.o: Assert.h AlignedFragment.o: AlignedFragment.h Utilities.h debian/manpages0000644000000000000000000000001711110210220010656 0ustar debian/proda.1 debian/watch0000644000000000000000000000013011110210220010165 0ustar version=3 opts="uversionmangle=s/_/\./" \ http://proda.stanford.edu/proda_(.*)\.tar\.gz debian/changelog0000644000000000000000000000734211735064015011050 0ustar proda (1.0-8) unstable; urgency=low [ Charles Plessy ] * Documented information in ‘debian/upstream’. * Removed mention of the bibliographic reference in ‘debian/control’. [ Andreas Tille ] * debian/control: - Replaced David Paleino as Uploader by myself because David seems to have dropped his name from all Debian Med packages - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Dropped quilt and cdbs from Build-Depends * debian/source/format: 3.0 (quilt) * debian/rules: short dh format -- Andreas Tille Thu, 29 Mar 2012 15:35:05 +0200 proda (1.0-7) unstable; urgency=low * debian/rules: swiched to CDBS (Closes: #486959). This delegates the support of parallel building to CDBS. * debian/control: - Added build-dependancy on CDBS. - Reverted to Standards-Version 3.7.3 because of lack of `debian/README.source' to explain the patch system. -- Charles Plessy Fri, 04 Jul 2008 12:43:43 +0900 proda (1.0-6) unstable; urgency=low * debian/patches/*.patch: documented and forwarded upstream. * debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch: Added `include ' to `AlignedFragment.h' (Closes: #486959). * debian/copyright: - Updated to the latest version of the machine-readable format. - Relicenced packaging to 'same as Proda itself'. - Added myself to the Hall of Fame. * debian/control: added myself as uploader. -- Charles Plessy Thu, 26 Jun 2008 13:27:54 +0900 proda (1.0-5) unstable; urgency=low Maintenance release. [ Charles Plessy ] * debian/proda.1.xml, debian/rules: semicosmetic change to indicate the path to the XSL stylesheet from within the XML source. [ David Paleino ] * debian/copyright updated to a machine-readable format. * debian/copyright-old removed * debian/control: - updated Standards-Version to 3.8.0 + enabled parallel building in debian/rules - updated debhelper dependency on >= 6 (also debian/compat) -- David Paleino Wed, 11 Jun 2008 15:08:30 +0200 proda (1.0-4) unstable; urgency=low * debian/patches - switching to quilt: - DPATCH: - 00list removed - 01-fix_gcc4.3_warnings.dpatch removed - 02-fix_CXXFLAGS.dpatch removed - QUILT: - series added - 01-fix_gcc4.3_warnings.patch added - 02-fix_CXXFLAGS.patch added - 03-fix_FTBFS_gcc4.3_missing_includes.patch added (closes: #455269) * debian/control - B-D updated, switching to quilt * debian/rules: - patch system updated, switching to quilt - adding "manpages" and "proda.1" rules for easier generation of the manpage in the future * debian/manpage.xml moved to debian/proda.1.xml * Updated Standards-Version to 3.7.3 -- David Paleino Sun, 16 Dec 2007 01:50:38 +0100 proda (1.0-3) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description. [ David Paleino ] * CXXFLAGS are no more hardcoded into the Makefile (added debian/patches/02-fix_CXXFLAGS.dpatch) * debian/control: removing dependencies for manpage generation - it is static now (there's no point in building always the same manpage on different archs) * debian/proda.1 added * debian/manpage.xml removed * debian/rules edited to reflect the changes above -- David Paleino Sun, 30 Sep 2007 10:12:28 +0200 proda (1.0-2) unstable; urgency=low * Fixed gcc4.3 warnings -- David Paleino Wed, 25 Apr 2007 20:59:04 +0200 proda (1.0-1) unstable; urgency=low * Initial release (Closes: #408347) -- David Paleino Tue, 24 Apr 2007 12:47:45 +0200 debian/rules0000755000000000000000000000003611735063045010251 0ustar #!/usr/bin/make -f %: dh $@