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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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