debian/changelog

+pilon (1.22+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille@debian.org>  Thu, 23 Feb 2017 16:48:18 +0100

debian/compat

+11

debian/control

+Source: pilon
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+               scala,
+               libscala-pickling-java
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/pilon
+Vcs-Git: https://salsa.debian.org/med-team/pilon.git
+Homepage: https://github.com/broadinstitute/pilon/wiki
+
+Package: pilon
+Architecture: all
+Depends: ${misc:Depends},
+         libhtsjdk-java
+Description: automated genome assembly improvement and variant detection tool
+ Pilon is a software tool which can be used to:
+  * Automatically improve draft assemblies
+  * Find variation among strains, including large event detection
+ Pilon requires as input a FASTA file of the genome along with one or more
+ BAM files of reads aligned to the input FASTA file. Pilon uses read
+ alignment analysis to identify inconsistencies between the input genome and
+ the evidence in the reads. It then attempts to make improvements to the
+ input genome, including:
+  * Single base differences
+  * Small indels
+  * Larger indel or block substitution events
+  * Gap filling
+  * Identification of local misassemblies, including optional opening
+    of new gaps

debian/copyright

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pilon
+Upstream-Contact: https://github.com/broadinstitute/pilon/issues
+Source: https://github.com/broadinstitute/pilon/releases
+Files-Excluded: lib/*
+
+Files: *
+Copyright: Copyright 2012-2017 Broad Institute, Inc.
+License: GPL-2
+
+Files: debian/*
+Copyright: 2018 Andreas Tille <tille@debian.org>
+License: GPL-2
+
+License: GPL-2
+ Pilon is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License version 2
+ as published by the Free Software Foundation.
+ .
+ Pilon 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 teyt of the GNU General
+ Public License at /usr/share/common-licenses/GPL-2.

debian/rules

+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+	dh $@

debian/source/format

+3.0 (quilt)

debian/upstream/metadata

+Reference:
+  Author: >
+     Bruce J. Walker and Thomas Abeel and Terrance Shea and Margaret Priest
+     and Amr Abouelliel and Sharadha Sakthikumar and Christina A. Cuomo and
+     Qiandong Zeng and Jennifer Wortman and Sarah K. Young and Ashlee M. Earl
+  Title: "Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement"
+  Journal: PLOSone
+  Year: 2014
+  Volume: 9
+  Number: 11
+  Pages: e11296
+  DOI: 10.1371/journal.pone.0112963
+  PMID: 25409509
+  URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112963
+  eprint: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0112963&type=printable

debian/watch

+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/broadinstitute/pilon/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)