debian/control

@@ -16,7 +16,9 @@ Package: ragout
 Architecture: any
 Depends: ${shlibs:Depends},
          ${python:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         sibelia,
+         python-networkx
 Description: Reference-Assisted Genome Ordering UTility
  Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
  chromosome-level scaffolding using multiple references. Given initial
@@ -31,3 +33,25 @@ Description: Reference-Assisted Genome Ordering UTility
  Ragout now supports both small and large genomes (of mammalian scale
  and complexity). The assembly of highly polymorphic genomes is
  currently limited.
+
+Package: ragout-examples
+Architecture: all
+Depends: ${shlibs:Depends},
+         ${python:Depends},
+         ${misc:Depends}
+Description: Reference-Assisted Genome Ordering UTility (example data)
+ Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
+ chromosome-level scaffolding using multiple references. Given initial
+ assembly fragments (contigs/scaffolds) and one or multiple related
+ references (complete or draft), it produces a chromosome-scale assembly
+ (as a set of scaffolds).
+ .
+ The approach is based on the analysis of genome rearrangements (like
+ inversions or chromosomal translocations) between the input genomes and
+ reconstructing the most parsimonious structure of the target genome.
+ .
+ Ragout now supports both small and large genomes (of mammalian scale
+ and complexity). The assembly of highly polymorphic genomes is
+ currently limited.
+ .
+ This package contains example data to test ragout.

debian/copyright

@@ -4,9 +4,52 @@ Source: https://github.com/fenderglass/Ragout/releases
 Files-Excluded: lib/networkx
 
 Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and
+                     Brian J. Raney and Ian Streeter and Matthew Dunn and
+                     Fengtang Yang and Duncan Odom and Paul Flicek and
+                     Thomas M. Keane and David Thybert and
+                     Benedict Paten and Son Pham
+License: BSD-3-clause
+
+Files: lib/newick/*
+Copyright: 2003-2008 Thomas Mailund <mailund@birc.au.dk>
+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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-2.
 
 Files: debian/*
 Copyright: 2019 Andreas Tille <tille@debian.org>
-License: <license>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * 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.
+    * Neither the name of the authors nor the
+      names of contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 AUTHORS 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.

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+         --name="Chromosome assembly with multiple references" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=ragout-maf2synteny
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=ragout-overlap
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="Constructs overlap graph from input contigsand outputs it in dot format" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/manpages

+debian/*.1

debian/patches/install_newick.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
+Description: Make sure newick is installed as well
+ Remark: This needs a hack in debian/rules - no idea how to do this more elegantly
+
+--- a/setup.py
++++ b/setup.py
+@@ -37,7 +37,8 @@ setup(name='ragout',
+       packages=['ragout', 'ragout/assembly_graph', 'ragout/breakpoint_graph',
+                 'ragout/maf2synteny', 'ragout/overlap', 'ragout/parsers',
+                 'ragout/phylogeny', 'ragout/scaffolder', 'ragout/shared',
+-                'ragout/synteny_backend'],
++                'ragout/synteny_backend',
++                'newick'],
+       package_data={'ragout': ['LICENSE']},
+       scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],
+       cmdclass={'build': MakeBuild}

debian/patches/series

+install_newick.patch

debian/ragout-examples.install

+examples	usr/share/doc/ragout

debian/ragout-maf2synteny.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH RAGOUT-MAF2SYNTENY "1" "February 2019" "ragout-maf2synteny 2.1.1" "User Commands"
+.SH NAME
+ragout-maf2synteny \- Reference-Assisted Genome Ordering UTility
+.SH SYNOPSIS
+.B maf2synteny
+[\fI\,-o out_dir\/\fR] [\fI\,-s simpl_params\/\fR] [\fI\,-m block_sizes\/\fR] \fI\,maf_file\/\fR
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+maf_file
+path to maf file
+.SS "optional arguments:"
+.TP
+\fB\-o\fR out_dir
+path to the output directory [default = .]
+.HP
+\fB\-s\fR simpl_params path to a file with custom simplification parameters [default = not set]
+.TP
+\fB\-b\fR block_sizes
+comma\-separated list of synteny block scales [default = 5000]
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/ragout-overlap.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH RAGOUT-OVERLAP "1" "February 2019" "ragout-overlap 2.1.1" "User Commands"
+.SH NAME
+ragout-overlap \- Reference-Assisted Genome Ordering UTility
+.SH SYNOPSIS
+.B overlap
+\fI\,fasta_in dot_out min_k max_k \/\fR[\fI\,--detect-kmer\/\fR] [\fI\,--hist\/\fR]
+.SH DESCRIPTION
+Constructs overlap graph from input contigsand outputs it in dot format
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/ragout.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH RAGOUT "1" "February 2019" "ragout 2.1.1" "User Commands"
+.SH NAME
+ragout \- Chromosome assembly with multiple references
+.SH SYNOPSIS
+.B ragout
+[\-h] [\-o output_dir] [\-s {sibelia,maf,hal}] [\-\-refine]
+[\-\-solid\-scaffolds] [\-\-overwrite] [\-\-repeats] [\-\-debug]
+[\-t THREADS] [\-\-version]
+recipe_file
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+recipe_file
+path to recipe file
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-o\fR output_dir, \fB\-\-outdir\fR output_dir
+output directory (default: ragout\-out)
+.TP
+\fB\-s\fR {sibelia,maf,hal}, \fB\-\-synteny\fR {sibelia,maf,hal}
+backend for synteny block decomposition (default:
+sibelia)
+.TP
+\fB\-\-refine\fR
+enable refinement with assembly graph (default: False)
+.TP
+\fB\-\-solid\-scaffolds\fR
+do not break input sequences \- disables chimera
+detection module (default: False)
+.TP
+\fB\-\-overwrite\fR
+overwrite results from the previous run (default:
+False)
+.TP
+\fB\-\-repeats\fR
+enable repeat resolution algorithm (default: False)
+.TP
+\fB\-\-debug\fR
+enable debug output (default: False)
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+number of threads for synteny backend (default: 1)
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/ragout.install

+usr

debian/rules

@@ -4,22 +4,20 @@
 export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@ --with python2 --buildsystem=pybuild
 
+override_dh_auto_clean:
+	dh_auto_clean
+	if [ -L newick  ] ; then rm newick ; fi
+
+override_dh_auto_configure:
+	ln -s lib/newick .
+	dh_auto_configure
+
 override_dh_install:
 	dh_install
 	find debian -name LICENSE -delete

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=ragout
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+gunzip -r *
+
+set -x
+ragout E.Coli/ecoli.rcp --outdir E.Coli/out/ --refine
+ragout H.Pylori/helicobacter.rcp --outdir H.Pylori/out/ --refine
+ragout S.Aureus/aureus.rcp --outdir S.Aureus/out/ --refine
+ragout V.Cholerae/cholerae.rcp --outdir V.Cholerae/out/ --refine