Andreas Tille pushed to branch master at Debian Med / pilon-non-free

Commits:
fb6a71cf by Andreas Tille at 2018-06-12T12:44:55+02:00
Initial packaging

- - - - -


9 changed files:

- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/get-orig-source
- + debian/rules
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch


Changes:

=====================================
debian/changelog
=====================================
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pilon-non-free (1.22-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <ti...@debian.org>  Thu, 23 Feb 2017 16:48:18 +0100


=====================================
debian/compat
=====================================
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+11


=====================================
debian/control
=====================================
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: pilon-non-free
+Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
+Uploaders: Andreas Tille <ti...@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/pilon-non-free
+Vcs-Git: https://salsa.debian.org/med-team/pilon-non-free.git
+Homepage: https://github.com/broadinstitute/pilon/wiki
+
+Package: pilon-non-free
+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
=====================================
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+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
+Comment: The code is actually free but currently there is no method
+         to build
+
+Files: *
+Copyright: Copyright 2012-2017 Broad Institute, Inc.
+License: GPL-2
+
+Files: debian/*
+Copyright: 2018 Andreas Tille <ti...@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/get-orig-source
=====================================
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,48 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+#        http://www.debian.org/doc/debian-policy/ch-source.html
+#        "get-orig-source (optional)"
+#        This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+#     source directory featuring the debian/ dir
+
+# Excluding files and repacking archives
+# --------------------------------------
+# See also mk-origtargz(1) and the --repack option to uscan(1), which
+# honor the Files-Excluded list in debian/copyright.
+# That may be all you need, especially since the repack option can be set
+# in debian/watch.
+
+# For an example how to fetch source from sourceforge SVN see
+#   https://anonscm.debian.org/git/debian-med/kmer-tools.git
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+    VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 
's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+    uscan --force-download --no-symlink
+else
+    VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) 
.*${NAME}.*?\1?"`
+    if echo "$VERSION" | grep -q "upstream-version" ; then
+        echo "Unable to parse version number"
+        exit
+    fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+mkdir ${TARDIR}
+mv ../pilon-${VERSION}.jar ${TARDIR}
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf 
"$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}


=====================================
debian/rules
=====================================
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+       dh $@
+
+get-orig-source:
+       . debian/get-orig-source


=====================================
debian/source/format
=====================================
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)


=====================================
debian/upstream/metadata
=====================================
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,15 @@
+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
=====================================
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/broadinstitute/pilon/releases 
.*/download/v.*/pilon-(\d[\d.-]+)\.jar



View it on GitLab: 
https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73
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