[med-svn] [reapr] 02/05: add debian dir
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sun Dec 13 18:45:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit 3239de86fe1449ecd3213977174e3b53ab55a70e
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sun Dec 13 13:26:33 2015 +0000
add debian dir
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 41 +++++++++++
debian/copyright | 29 ++++++++
debian/patches/hardening | 150 +++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/patches/use_shared_libs | 135 +++++++++++++++++++++++++++++++++++++
debian/rules | 15 +++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++
debian/watch | 3 +
11 files changed, 394 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d19f192
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+reapr (1.0.18+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 12 Dec 2015 19:47:37 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..ca44b4b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,41 @@
+Source: reapr
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libbamtools-dev,
+ libtabixpp-dev,
+ libhts-dev,
+ zlib1g-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/reapr.git
+Vcs-Git: git://anonscm.debian.org/debian-med/reapr.git
+Homepage: http://www.sanger.ac.uk/science/tools/reapr
+
+Package: reapr
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ samtools,
+ bamtools,
+ smalt,
+ r-base,
+ snpomatic,
+ tabix,
+ libfile-copy-link-perl
+Description: evaluation of genome assemblies using mapped paired end reads
+ REAPR is a tool that evaluates the accuracy of a genome assembly using mapped
+ paired end reads, without the use of a reference genome for comparison. It can
+ be used in any stage of an assembly pipeline to automatically break incorrect
+ scaffolds and flag other errors in an assembly for manual inspection. It
+ reports mis-assemblies and other warnings, and produces a new broken assembly
+ based on the error calls.
+ .
+ The software requires as input an assembly in FASTA format and paired reads
+ mapped to the assembly in a BAM file. Mapping information such as the fragment
+ coverage and insert size distribution is analysed to locate mis-assemblies.
+ REAPR works best using mapped read pairs from a large insert library (at least
+ 1000bp). Additionally, if a short insert Illumina library is also available,
+ REAPR can combine this with the large insert library in order to score each
+ base of the assembly.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..452512c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: REAPR
+Source: http://www.sanger.ac.uk/science/tools/reapr
+Files-Excluded: third_party/* manual.pdf
+
+Files: *
+Copyright: © 2013-2015 Genome Research Ltd.
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2015 Sascha Steinbiss <sascha at steinbiss.name>
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..8d0d57c
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,150 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,5 +1,5 @@
+ CC = g++
+-CFLAGS = -Wall -O3 -I /usr/include/bamtools -I /usr/include
++CFLAGS += -Wall -O3 -I /usr/include/bamtools -I /usr/include
+ TABIX = -ltabixpp -lhts -lz
+ STATS_OBJS = trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
+ SCORE_OBJS = errorWindow.o utils.o histogram.o
+@@ -19,106 +19,106 @@
+ all: $(EXECUTABLES)
+
+ errorWindow.o: errorWindow.cpp
+- $(CC) $(CFLAGS) -c errorWindow.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c errorWindow.cpp
+
+ trianglePlot.o: trianglePlot.cpp utils.o
+- $(CC) $(CFLAGS) -c trianglePlot.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c trianglePlot.cpp
+
+ coveragePlot.o: coveragePlot.cpp
+- $(CC) $(CFLAGS) -c coveragePlot.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c coveragePlot.cpp
+
+ fasta.o: fasta.cpp
+- $(CC) $(CFLAGS) -c fasta.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c fasta.cpp
+
+ histogram.o: histogram.cpp
+- $(CC) $(CFLAGS) -c histogram.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c histogram.cpp
+
+ utils.o: utils.cpp
+- $(CC) $(CFLAGS) -c utils.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c utils.cpp
+
+ task_stats: task_stats.o $(STATS_OBJS)
+- $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools $(TABIX) -o task_stats
++ $(CC) $(CPPFLAGS) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools $(TABIX) -o task_stats $(LDFLAGS)
+
+ task_stats.o: task_stats.cpp $(STATS_OBJS)
+- $(CC) $(CFLAGS) -c task_stats.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c task_stats.cpp
+
+ task_score: task_score.o $(SCORE_OBJS)
+- $(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX)
++ $(CC) -o task_score $(CPPFLAGS) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX) $(LDFLAGS)
+
+ task_score.o: task_score.cpp $(SCORE_OBJS)
+- $(CC) $(CFLAGS) -c task_score.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c task_score.cpp
+
+ task_break: task_break.o $(BREAK_OBJS)
+- $(CC) $(CFLAGS) task_break.o -lbamtools $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break
++ $(CC) $(CPPFLAGS) $(CFLAGS) task_break.o -lbamtools $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break $(LDFLAGS)
+
+ task_break.o: task_break.cpp $(BREAK_OBJS)
+- $(CC) $(CFLAGS) -c task_break.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c task_break.cpp
+
+ bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS)
+- $(CC) $(CFLAGS) bam2fragCov.o -lbamtools $(BAM2COV_OBJS) -lbamtools $(TABIX) -o bam2fragCov
++ $(CC) $(CPPFLAGS) $(CFLAGS) bam2fragCov.o -lbamtools $(BAM2COV_OBJS) -lbamtools $(TABIX) -o bam2fragCov $(LDFLAGS)
+
+ bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS)
+- $(CC) $(CFLAGS) -c bam2fragCov.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c bam2fragCov.cpp
+
+ bam2insert: bam2insert.o $(BAM2INSERT_OBJS)
+- $(CC) $(CFLAGS) bam2insert.o -lbamtools $(BAM2INSERT_OBJS) -lbamtools $(TABIX) -o bam2insert
++ $(CC) $(CPPFLAGS) $(CFLAGS) bam2insert.o -lbamtools $(BAM2INSERT_OBJS) -lbamtools $(TABIX) -o bam2insert $(LDFLAGS)
+
+ bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS)
+- $(CC) $(CFLAGS) -c bam2insert.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c bam2insert.cpp
+
+ bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS)
+- $(CC) $(CFLAGS) bam2perfect.o -lbamtools $(BAM2PERFECT_OBJS) -lbamtools $(TABIX) -o bam2perfect
++ $(CC) $(CPPFLAGS) $(CFLAGS) bam2perfect.o -lbamtools $(BAM2PERFECT_OBJS) -lbamtools $(TABIX) -o bam2perfect $(LDFLAGS)
+
+ bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS)
+- $(CC) $(CFLAGS) -c bam2perfect.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c bam2perfect.cpp
+
+ bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
+- $(CC) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate
++ $(CC) $(CPPFLAGS) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate $(LDFLAGS)
+
+ bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
+- $(CC) $(CFLAGS) -c bam2fcdEstimate.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c bam2fcdEstimate.cpp
+
+ make_plots: make_plots.o
+- $(CC) $(CFLAGS) make_plots.o -o make_plots
++ $(CC) $(CPPFLAGS) $(CFLAGS) make_plots.o -o make_plots $(LDFLAGS)
+
+ make_plots.o: make_plots.cpp
+- $(CC) $(CFLAGS) -c make_plots.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c make_plots.cpp
+
+ fa2gc: fa2gc.o $(FA2GC_OBJS)
+- $(CC) $(CFLAGS) fa2gc.o $(FA2GC_OBJS) -o fa2gc
++ $(CC) $(CPPFLAGS) $(CFLAGS) fa2gc.o $(FA2GC_OBJS) -o fa2gc $(LDFLAGS)
+
+ fa2gc.o: fa2gc.cpp $(FA2GC_OBJS)
+- $(CC) $(CFLAGS) -c fa2gc.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c fa2gc.cpp
+
+ fa2gaps: fa2gaps.o $(FA2GAPS_OBJS)
+- $(CC) $(CFLAGS) fa2gaps.o $(FA2GAPS_OBJS) -o fa2gaps
++ $(CC) $(CPPFLAGS) $(CFLAGS) fa2gaps.o $(FA2GAPS_OBJS) -o fa2gaps $(LDFLAGS)
+
+ fa2gaps.o: fa2gaps.cpp $(FA2GAPS_OBJS)
+- $(CC) $(CFLAGS) -c fa2gaps.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c fa2gaps.cpp
+
+ n50: n50.o $(N50_OBJS)
+- $(CC) $(CFLAGS) n50.o $(N50_OBJS) -o n50
++ $(CC) $(CPPFLAGS) $(CFLAGS) n50.o $(N50_OBJS) -o n50 $(LDFLAGS)
+
+ n50.o: n50.cpp $(N50_OBJS)
+- $(CC) $(CFLAGS) -c n50.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c n50.cpp
+
+ scaff2contig: scaff2contig.o $(SCAFF2CONTIG_OBJS)
+- $(CC) $(CFLAGS) scaff2contig.o $(SCAFF2CONTIG_OBJS) -o scaff2contig
++ $(CC) $(CPPFLAGS) $(CFLAGS) scaff2contig.o $(SCAFF2CONTIG_OBJS) -o scaff2contig $(LDFLAGS)
+
+ scaff2contig.o: scaff2contig.cpp $(SCAFF2CONTIG_OBJS)
+- $(CC) $(CFLAGS) -c scaff2contig.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c scaff2contig.cpp
+
+ task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
+- $(CC) $(CFLAGS) task_gapresize.o -lbamtools $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize
++ $(CC) $(CPPFLAGS) $(CFLAGS) task_gapresize.o -lbamtools $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize $(LDFLAGS)
+
+ task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
+- $(CC) $(CFLAGS) -c task_gapresize.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c task_gapresize.cpp
+
+ task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
+- $(CC) $(CFLAGS) task_fcdrate.o -lbamtools $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate
++ $(CC) $(CPPFLAGS) $(CFLAGS) task_fcdrate.o -lbamtools $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate $(LDFLAGS)
+
+ task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
+- $(CC) $(CFLAGS) -c task_fcdrate.cpp
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c task_fcdrate.cpp
+
+ clean:
+ rm -rf *.o $(EXECUTABLES)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..ffad062
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+use_shared_libs
+hardening
diff --git a/debian/patches/use_shared_libs b/debian/patches/use_shared_libs
new file mode 100644
index 0000000..1f1d009
--- /dev/null
+++ b/debian/patches/use_shared_libs
@@ -0,0 +1,135 @@
+Description: Use_shared_libs
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,6 @@
+-BAMTOOLS_ROOT = $(CURDIR)/bamtools
+ CC = g++
+-CFLAGS = -Wl,-rpath,$(BAMTOOLS_ROOT)/lib -Wall -O3 -I $(BAMTOOLS_ROOT)/include -L $(BAMTOOLS_ROOT)/lib
+-TABIX = tabix/tabix.o -L./tabix -ltabix -lz
++CFLAGS = -Wall -O3 -I /usr/include/bamtools -I /usr/include
++TABIX = -ltabixpp -lhts -lz
+ STATS_OBJS = trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
+ SCORE_OBJS = errorWindow.o utils.o histogram.o
+ BREAK_OBJS = fasta.o utils.o
+@@ -35,46 +34,46 @@
+ $(CC) $(CFLAGS) -c histogram.cpp
+
+ utils.o: utils.cpp
+- $(CC) $(CFLAGS) -lbamtools -c utils.cpp
++ $(CC) $(CFLAGS) -c utils.cpp
+
+ task_stats: task_stats.o $(STATS_OBJS)
+- $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools -o task_stats $(TABIX)
++ $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools $(TABIX) -o task_stats
+
+ task_stats.o: task_stats.cpp $(STATS_OBJS)
+ $(CC) $(CFLAGS) -c task_stats.cpp
+
+ task_score: task_score.o $(SCORE_OBJS)
+- $(CC) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools -o task_score $(TABIX)
++ $(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX)
+
+ task_score.o: task_score.cpp $(SCORE_OBJS)
+ $(CC) $(CFLAGS) -c task_score.cpp
+
+ task_break: task_break.o $(BREAK_OBJS)
+- $(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools -o task_break $(TABIX)
++ $(CC) $(CFLAGS) task_break.o -lbamtools $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break
+
+ task_break.o: task_break.cpp $(BREAK_OBJS)
+ $(CC) $(CFLAGS) -c task_break.cpp
+
+ bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS)
+- $(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) -lbamtools -o bam2fragCov $(TABIX)
++ $(CC) $(CFLAGS) bam2fragCov.o -lbamtools $(BAM2COV_OBJS) -lbamtools $(TABIX) -o bam2fragCov
+
+ bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS)
+ $(CC) $(CFLAGS) -c bam2fragCov.cpp
+
+ bam2insert: bam2insert.o $(BAM2INSERT_OBJS)
+- $(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) -lbamtools -o bam2insert $(TABIX)
++ $(CC) $(CFLAGS) bam2insert.o -lbamtools $(BAM2INSERT_OBJS) -lbamtools $(TABIX) -o bam2insert
+
+ bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS)
+ $(CC) $(CFLAGS) -c bam2insert.cpp
+
+ bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS)
+- $(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) -lbamtools -o bam2perfect $(TABIX)
++ $(CC) $(CFLAGS) bam2perfect.o -lbamtools $(BAM2PERFECT_OBJS) -lbamtools $(TABIX) -o bam2perfect
+
+ bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS)
+ $(CC) $(CFLAGS) -c bam2perfect.cpp
+
+ bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
+- $(CC) $(CFLAGS) bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -lbamtools -o bam2fcdEstimate $(TABIX)
++ $(CC) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate
+
+ bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
+ $(CC) $(CFLAGS) -c bam2fcdEstimate.cpp
+@@ -110,13 +109,13 @@
+ $(CC) $(CFLAGS) -c scaff2contig.cpp
+
+ task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
+- $(CC) $(CFLAGS) task_gapresize.o $(GAPRESIZE_OBJS) -lbamtools -o task_gapresize $(TABIX)
++ $(CC) $(CFLAGS) task_gapresize.o -lbamtools $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize
+
+ task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
+ $(CC) $(CFLAGS) -c task_gapresize.cpp
+
+ task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
+- $(CC) $(CFLAGS) task_fcdrate.o $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(TABIX)
++ $(CC) $(CFLAGS) task_fcdrate.o -lbamtools $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate
+
+ task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
+ $(CC) $(CFLAGS) -c task_fcdrate.cpp
+--- a/src/task_break.cpp
++++ b/src/task_break.cpp
+@@ -10,7 +10,6 @@
+ #include <assert.h>
+ #include "fasta.h"
+ #include "utils.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace std;
+
+--- a/src/task_score.cpp
++++ b/src/task_score.cpp
+@@ -18,7 +18,6 @@
+ #include "histogram.h"
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace BamTools;
+ using namespace std;
+--- a/src/task_stats.cpp
++++ b/src/task_stats.cpp
+@@ -18,7 +18,6 @@
+ #include "utils.h"
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace BamTools;
+ using namespace std;
+--- a/src/utils.h
++++ b/src/utils.h
+@@ -11,7 +11,7 @@
+
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
++#include "tabix.hpp"
+
+ const short INNIE = 1;
+ const short OUTTIE = 2;
+--- a/src/task_fcdrate.cpp
++++ b/src/task_fcdrate.cpp
+@@ -9,7 +9,6 @@
+
+ #include "utils.h"
+ #include "histogram.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace std;
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..25348b1
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd src && $(MAKE)
+
+override_dh_auto_install:
+ mkdir -p debian/reapr/usr/lib
+ find src -name 'task*' -and -executable -exec cp {} debian/reapr/usr/lib \;
+ mkdir -p debian/reapr/usr/bin
+ cp src/reapr.pl debian/reapr/usr/bin/reapr
\ No newline at end of file
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..5a6ba62
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman and Thomas D Otto
+ Title: REAPR: a universal tool for genome assembly evaluation
+ Journal: Genome Biology
+ Year: 2013
+ Volume: 14
+ Number: 5
+ Pages: R47
+ DOI: 10.1186/gb-2013-14-5-r47
+ PMID: 23710727
+ URL: http://www.genomebiology.com/2013/14/5/R47/
+ eprint: http://www.genomebiology.com/content/pdf/gb-2013-14-5-r47.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a8a0612
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=pasv,repacksuffix=+dsfg,dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$// \
+ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_([0-9.]+)\.tar\.gz
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