debian/0000755000000000000000000000000011745723206007175 5ustar debian/upstream0000644000000000000000000000112411745713424010757 0ustar Contact: Kirill Rotmistrovsky Name: e-PCR Homepage: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/ Reference: author: Schuler, Gregory D. title: Sequence Mapping by Electronic PCR journal: Genome Research volume: 7 number: 5 pages: 541-550 doi: 10.1101/gr.7.5.541 year: 1997 URL: http://genome.cshlp.org/content/7/5/541.abstract eprint: http://genome.cshlp.org/content/7/5/541.full.pdf+html PMID: 9149949 Watch: | version=3 ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-(.*)-src\.tar\.gz Webservice: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/ debian/source/0000755000000000000000000000000011745071217010473 5ustar debian/source/format0000644000000000000000000000001411467561373011711 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000456011745713424011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: e-PCR Upstream-Contact: Kirill Rotmistrovsky Source: ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-2.3.12-src.tar.gz Files: * Copyright: nobody License: public-domain PUBLIC DOMAIN NOTICE National Center for Biotechnology Information . This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. . Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. . Please cite the author in any work or product based on this material. Files: debian/* Copyright: © 2003-2004 Steffen Moeller © 2008-2012 Andreas Tille © 2008-2009 Charles Plessy License: GPL-2+ 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 systems, you can find the full text of the GNU General Public License version 2 in the file `/usr/share/common-licenses/GPL-2' debian/compat0000644000000000000000000000000211745073251010371 0ustar 9 debian/ncbi-epcr.docs0000644000000000000000000000002711110210623011664 0ustar README.txt README.html debian/control0000644000000000000000000000333411745714633010607 0ustar Source: epcr Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Homepage: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/epcr/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/epcr/trunk/ Package: ncbi-epcr Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: bioperl Description: Tool to test a DNA sequence for the presence of sequence tagged sites Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs. . The new version of e-PCR implements a fuzzy matching strategy. To reduce likelihood that a true STS will be missed due to mismatches, multiple discontigous words may be used instead of a single exact word. Each of this word has groups of significant positions separated by 'wildcard' positions that are not required to match. In addition, it is also possible to allow gaps in the primer alignments. . The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database. debian/famap.10000644000000000000000000000300011667613732010341 0ustar .TH FASTA "1" "April 2008" "Fasta converter for e-PCR version 2.3.9" "User Commands" .SH NAME famap \- prepare Fasta sequence database for re-PCR searches .SH SYNOPSIS famap [\-hV] \fB\-b\fR mmapped\-file [\-t cvt] [fafile ...] .PP famap [\-hV] \fB\-d\fR mmapped\-file [ord ...] .PP famap [\-hV] \fB\-l\fR mmapped\-file [ord ...] .SH DESCRIPTION The program .B famap is part of the e-PCR suite and is used to build mmapped-file from FASTA files for reverse e-PCR searches .SH OPTIONS where cvt (conversion table) is one of: .IP off \- as is (default) .IP n \- nucleotide [acgtnACGTN] allowed, .IP N \- nucleotide uppercase allowed [ACGTN] .IP nx \- nucleotide with ambiguity codes allowed .IP NX \- nucleotide with ambiguity codes uppercase .SH "EXAMPLE" .PP famap -tN -b genome.famap org/chr_*.fa .PP fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap .PP re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200 See famap(1) and re-pcr(1) .SH "SEE ALSO" .PP /usr/share/doc/ncbi-epcr/README.txt .PP bioperl(1), e-pcr(1), famap(1) and re-pcr(1) .PP .SH "AUTHORS" .PP This manual page was written by Andreas Tille for the \fBDebian\fP 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. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/patches/0000755000000000000000000000000011745715317010630 5ustar debian/patches/fix_header_location.patch0000644000000000000000000000053011530676255015634 0ustar Author: Andreas Tille Date: Tue, 22 Feb 2011 09:09:21 +0100 Description: Fix path of includes --- epcr-2.3.12.orig/faread.cpp +++ epcr-2.3.12/faread.cpp @@ -31,7 +31,8 @@ #include #include -#include +#include +#include #include #include debian/patches/series0000644000000000000000000000014611745715170012043 0ustar fix_clean_target.patch fix_header_location.patch ensure_build_options.patch use-dpkg-buildflags.patch debian/patches/fix_clean_target.patch0000644000000000000000000000077711530673325015154 0ustar Author: Andreas Tille Date: Tue, 22 Feb 2011 09:09:21 +0100 Description: Do not let clean target fail if there is nothing to clean --- epcr-2.3.12.orig/stand/config.mk +++ epcr-2.3.12/stand/config.mk @@ -94,13 +94,13 @@ done clean: - -rm $(OBJ) $(HDR:%=%~) $(SRC:%=%~) + -rm -f $(OBJ) $(HDR:%=%~) $(SRC:%=%~) clean-all: clean - -rm $(TARGET) + -rm -f $(TARGET) dist-clean: clean-all - -rm *~ + -rm -f *~ -test -L $(LIBNAME) && rm $(LIBNAME) $(objdir)/%.o: $(srcdir)/%.cpp debian/patches/use-dpkg-buildflags.patch0000644000000000000000000000101611745715317015500 0ustar Description: Use build flags from environment (dpkg-buildflags). Necessary for hardening flags. Author: Andreas Tille Last-Update: 2012-04-25 --- e-PCR-2.3.12.orig/stand/config.mk +++ e-PCR-2.3.12/stand/config.mk @@ -104,7 +104,7 @@ -test -L $(LIBNAME) && rm $(LIBNAME) $(objdir)/%.o: $(srcdir)/%.cpp - $(CXX) $(CXXFLAGS) -c $< -o $@ + $(CXX) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $< -o $@ ######################################################################## ## $Log: config.mk,v $ debian/patches/ensure_build_options.patch0000644000000000000000000000051311530711435016070 0ustar --- e-PCR-2.3.12.orig/Makefile +++ e-PCR-2.3.12/Makefile @@ -29,7 +29,7 @@ all links dirs clean dist clean-all install install-lib dist-clean depend: for i in $(LIBS:%=lib%) $(BINS) ; do \ - $(MAKE) -ef $(srcdir)/stand/Makefile.$$i $@ ; \ + $(MAKE) -ef $(srcdir)/stand/Makefile.$$i CXXFLAGS='$(CFLAGS)' $@ ; \ done # debian/watch0000644000000000000000000000011711110210623010201 0ustar version=3 ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-(.*)-src\.tar\.gz debian/re-PCR.10000644000000000000000000000524311110210623010267 0ustar .TH "RE-PCR" "1" "April 2008" .SH "NAME" re-PCR \(em Find sequence tagged sites (STS) in DNA sequences .SH "SYNOPSIS" .PP .B re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...] .B re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...] .B re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]] .B re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...] .SH "DESCRIPTION" .PP Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by performing STS and primer searches. .SH "OPTIONS" .PP .IP "\fB-p=\fIhash-file\fR\fP " 10 Perform primer lookup using hash-file .IP "\fB-P=\fIhash-file\fR\fP " 10 Perform primer lookup using hash-file .IP "\fB-s=\fIhash-file\fR\fP " 10 Perform STS lookup using hash-file .IP "\fB-S=\fIhash-file\fR\fP " 10 Perform STS lookup using hash-file .IP "\fB-n=\fImism\fR\fP " 10 Set max allowed mismatches per primer for lookup .IP "\fB-g=\fIgaps\fR\fP " 10 Set max allowed indels per primer for lookup .IP "\fB-m=\fImargin\fR\fP " 10 Set variability for STS size for lookup .IP "\fB-l\fP " 10 Use presize alignments (only if gaps>0) .IP "\fB-G\fP " 10 Print alignments in comments .IP "\fB-d=\fImin-max\fR\fP " 10 Set default STS size .IP "\fB-r=\fI+|-\fR\fP " 10 Enable/disable reverse STS lookup .IP "\fB-O=\fI+|-\fR\fP " 10 Enable/disable syscall optimisation .IP "\fB-C=\fIbatchcnt\fR\fP " 10 Set number of STSes per batch .IP "\fB-o=\fIoutfile\fR\fP " 10 Set output file name .IP "\fB-q\fP " 10 Quiet (no progress indicator) .SH "EXAMPLE" .PP famap -tN -b genome.famap org/chr_*.fa .PP fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap .PP re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200 See famap(1) and fahash(1) .SH "SEE ALSO" .PP /usr/share/doc/ncbi-epcr/README.txt .PP bioperl(1), e-pcr(1), famap(1) and fahash(1) .PP .SH "AUTHORS" .PP This manual page was written by Andreas Tille for the \fBDebian\fP 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. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/e-PCR.10000644000000000000000000000600311667613732010131 0ustar .TH "E-PCR" "1" "February 2004" .SH "NAME" e-PCR \(em Find sequence tagged sites (STS) in DNA sequences .SH "SYNOPSIS" .PP \fBe-PCR [-hV] [posix-options] stsfile [fasta ...]\fR [\fB\fIcompat-options\fR\fP] .SH "DESCRIPTION" .PP The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product. .SH "OPTIONS" .PP posix-options are: .IP "\fB-m=\fI##\fR\fP " 10 Margin (default 50) .IP "\fB-w=\fI##\fR\fP " 10 Wordsize (default 7) .IP "\fB-n=\fI##\fR\fP " 10 Max mismatches allowed (default 0) .IP "\fB-g=\fI##\fR\fP " 10 Max indels allowed (default 0) .IP "\fB-f=\fI##\fR\fP " 10 Use ## disontiguous words, slow if ##>1 .IP "\fB-o=\fI##\fR\fP " 10 Set output file .IP "\fB-t=\fI##\fR\fP " 10 Set output format: .IP "" 10 1 - classic, range (pos1..pos2) .IP "" 10 2 - classic, midpoint .IP "" 10 3 - tabular .IP "" 10 4 - tabular with alignment in comments (slow) .IP "\fB-d=\fI##-##\fR\fP " 10 Set default size range (default 100-350) .IP "\fB-p=\fI+-\fR\fP " 10 Turn hits postprocess on/off .IP "\fB-v=\fI##\fR\fP " 10 Verbosity flags .IP "\fB-a=\fIa|f\fR\fP " 10 Use presize alignments (only if gaps>0), slow .IP "" 10 a - Always or f - as Fallback .IP "\fB-x=\fI+-\fR\fP " 10 Use 5'-end lowercase masking of primers (default -) .IP "\fB-u=\fI+-\fR\fP " 10 Uppercase all primers (default -) .P compat-options (duplicate posix-options) are .IP "\fBM=\fI##\fR\fP " 10 Margin (default 50) .IP "\fBW=\fI##\fR\fP " 10 Wordsize (default 7) .IP "\fBN=\fI##\fR\fP " 10 Number of mismatches allowed (default 0) .IP "\fBG=\fI##\fR\fP " 10 Max indels allowed (default 0) .IP "\fBF=\fI##\fR\fP " 10 Use ## discontinuous words .IP "\fBO=\fI##\fR\fP " 10 Set output file to ## .IP "\fBT=\fI##\fR\fP " 10 Set output format (1..3) .IP "\fBD=\fI##-##\fR\fP " 10 Set default size range .IP "\fBP=\fI+-\fR\fP " 10 Postprocess hits on/off .IP "\fBV=\fI##\fR\fP " 10 Verbosity flags .IP "\fBA=\fIa|f\fR\fP " 10 Use presize alignments (only if gaps>0), slow .IP "" 10 a - Always or f - as Fallback .IP "\fBX=\fI+-\fR\fP " 10 Use 5'-end lowercase masking of primers (default -) .IP "\fBU=\fI+-\fR\fP " 10 Uppercase all primers (default -) .IP "\fB-mid\fP " 10 Same as T=2 .P For information about further options just call \fBe-PCR\fR without any options. .SH "SEE ALSO" .PP /usr/share/doc/ncbi-epcr/README.txt .PP bioperl(1), re-pcr(1) .PP .SH "AUTHORS" .PP This manual page was written by Steffen Moeller and Andreas Tille for the \fBDebian\fP 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. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/changelog0000644000000000000000000001202311745723111011040 0ustar epcr (2.3.12-1-1) unstable; urgency=low * New upstream version that has applied debian/patches/gcc-4.7.patch (so this patch was removed) * debian/copyright: Add Upstream-Name & Upstream-Contact * debian/control: SVN dir was renamed from ncbi-epcr to epcr * debian/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS hardening flags * debian/rules: - do not specify fixed version strings but rather obtain these via dpkg-parsechangelog - Enable hardening flags -- Andreas Tille Wed, 25 Apr 2012 08:27:20 +0200 epcr (2.3.12-3) unstable; urgency=low [ A. Costa ] * Corrected typos in manpages (Closes: #650476). [ Charles Plessy ] * Lifted debian/copyright to latest DEP 5 draft. [ Andreas Tille ] * debian/upstream: Took over references from debian/reference and debian/README.Debian * debian/control: - Standards-Version: 3.9.3 - Fixed Vcs fields * debian/{control,rules}: Removed explicite dependency from quilt * debian/patches/gcc-4.7.patch: Add missing include to build using gcc-4.7 Closes: #667156 * debian/copyright: Fix DEP5 and verify using cme fix dpkg-copyright * debhelper 9 (control+compat) -- Andreas Tille Sun, 22 Apr 2012 22:52:29 +0200 epcr (2.3.12-2) unstable; urgency=low * debian/source/format: 3.0 (quilt) * Standards-Version: 3.9.1 (no changes needed) * debian/rules: Implementation of upstream build systems seems to be simpler with short dh rules file * debian/patches: Ensure Build options will be propagated properly Closes: 614482 -- Andreas Tille Tue, 22 Feb 2011 09:09:21 +0100 epcr (2.3.12-1) unstable; urgency=low * New upstream release buildable with GCC 4.4 (Closes: #504849) * Version number updated in debian/rules. * debian/copyright refreshed to my latest exploration of the machine-readable format. * Added a BibTeX reference in debian/reference. -- Charles Plessy Thu, 02 Jul 2009 09:31:29 +0900 epcr (2.3.11-1) unstable; urgency=low * New upstream release. When parsing commandline if -d was used before -w or -f default size was reset to program's default. [ Andreas Tille ] * debian/control: - Fixed Vcs-Svn (missing svn/) - Updated Standards-Version to 3.8.2 (no changes needed) [ Charles Plessy ] * debian/control: - Added myself to the Uploaders. - Using Debhelper 7 (also in debian/compat). - Removed patch system (also in debian/rules). -- Charles Plessy Thu, 18 Jun 2009 17:39:15 +0900 epcr (2.3.10-1) unstable; urgency=low [ Charles Plessy ] * New upstream release applying Andreases patches introduced in the previous Debian package. * debian/patches: removed 10_assert.patch and 10_gcc4.3.patch (Removed debian/patches/series as well.) * debian/copyright converted to machine-readable format. * debian/control: downgraded recommendation on bioperl to `Suggests:' because BioPerl provides a parser for e-PCR results, but e-PCR does not need BioPerl for running. [ Andreas Tille ] * Raised from priority extra to optional according to policy. * Standards-Version: 3.8.0 (no changes needed) -- Andreas Tille Fri, 06 Jun 2008 09:10:38 +0200 epcr (2.3.9-1) unstable; urgency=low * New upstream version Closes: #385256 Upstream correctly handles strip option so this also Closes: #436815 * There are no reasonable files targetting at a ncbi-epcr-data package and thus this is dropped Closes: #241710 because the issue of this bug becomes void * Group maintenance by Debian-Med team - DM-Upload-Allowed: Yes - Vcs tags - Use correct address as Uploader: Steffen Moeller * Removed [Biology] from short description * Moved Homepage from long description to control fields and fixed Homepage * Standards-Version: 3.7.3 (no changes needed) * debhelper >= 5 * Patches using quilt * Use cdbs * Updated long description according to text on web Homepage * Just use (and fix) the docbook-to-man output rather than live with the broken output * Wrote man pages for re-PCR and fahash * -- Andreas Tille Wed, 16 Apr 2008 14:38:00 +0200 epcr (1.2.0-3) unstable; urgency=low * Added patch for compilation on Alpha (presumably) and IA64 (patch by Sebastian Muszynski, thanks also go to Lamont Jones) (Closes: #239733). * data package is now architecture-independent (Closes: #233421). -- Steffen Moeller Thu, 20 Feb 2004 12:50:19 +0100 epcr (1.2.0-2) unstable; urgency=low * Corrected structure of man page * Reduced number of ignored errors during build process to ease automated interpretation of buildd logs -- Steffen Moeller Thu, 20 Feb 2004 12:50:19 +0100 epcr (1.2.0-1) unstable; urgency=low * Initial Release (Closes:#221847). * Separated samples and databases to -data package -- Steffen Moeller Thu, 20 Nov 2003 12:50:19 +0100 debian/fahash.10000644000000000000000000000357311110210623010475 0ustar .TH FAHASH "1" "April 2008" "Reverse e-PCR: sequence hash builder version 2.3.9" "User Commands" .SH NAME fahash \- sequence hash builder for reverse e-PCR .SH SYNOPSIS fahash [\-hV] \fB\-b\fR hash\-file [\-w wdsize] [\-f period] [\-F fragment_min,fragment_max] [\-k] [\-c cachesize] [\-v 1|2] famap\-file ... .PP fahash [\-hV] \fB\-T\fR hash\-file [\-o outfile] .SH DESCRIPTION The program .B fahash is part of the e-PCR suite and is used to build hash-files, and output word usage statistics for reverse e-PCR searches. .SH OPTIONS .TP \fB\-b\fR hash\-file Build hash tables (hash\-file) from sequence files, .TP \fB\-T\fR hash\-file Print word usage statistics for hash\-file .TP \fB\-o\fR outfile Write output to file `outfile' .SS "build-options:" .TP \fB\-w\fR wordsize Set word size when building hash tables .TP \fB\-f\fR period Set discontiguity when building hash tables .TP \fB\-k\fR Skip repeats when building hash\-file .TP \fB\-F\fR min,max Set watermarks for fragment size (in Mb) (version 1 only) .TP \fB\-c\fR cachesize Set cache size (version 2 only) .TP \fB\-v\fR ver Use format version (1|2, 2 is default) .SH "EXAMPLE" .PP famap -tN -b genome.famap org/chr_*.fa .PP fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap .PP re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200 See famap(1) and re-pcr(1) .SH "SEE ALSO" .PP /usr/share/doc/ncbi-epcr/README.txt .PP bioperl(1), e-pcr(1), famap(1) and re-pcr(1) .PP .SH "AUTHORS" .PP This manual page was written by Andreas Tille for the \fBDebian\fP 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. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/rules0000755000000000000000000000144611745723067010267 0ustar #!/usr/bin/make -f # debian/rules for ncbi-epcr using # Andreas Tille , GPL VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') VER_MAJOR := $(shell echo $(VERSION) | sed 's/^\([0-9]\+\)\..*/\1/') VER_MINOR := $(shell echo $(VERSION) | sed 's/^[0-9]\+\.\([0-9]\+\)\..*/\1/') VER_BUILD := $(shell echo $(VERSION) | sed 's/^[0-9]\+\.[0-9]\+\.\(.*\)/\1/') CFLAGS += -I. -g2 -DDEALLOCATE=0 -DVERSION=\"$(VERSION)\" -DVER_MAJOR=$(VER_MAJOR) -DVER_MINOR=$(VER_MINOR) -DVER_BUILD=$(VER_BUILD) -DSTANDALONE=1 LDFLAGS += -L. %: dh $@ override_dh_auto_clean: rm -fr epcr rm -f *_depend.mk rm -f libepcr.a *.o rm -f e-PCR famap fahash re-PCR override_dh_auto_build: $(MAKE) links depend all OPTIMIZE=6 override_dh_auto_install: # do nothing debian/ncbi-epcr.install0000644000000000000000000000010011110210623012372 0ustar e-PCR usr/bin famap usr/bin fahash usr/bin re-PCR usr/bin debian/ncbi-epcr.manpages0000644000000000000000000000001311110210623012522 0ustar debian/*.1