[med-svn] [Git][med-team/pilon][master] 2 commits: Initial packaging

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / pilon


Commits:
f40fb01e by Andreas Tille at 2018-05-25T12:28:55+02:00
Initial packaging

- - - - -
2638288b by Andreas Tille at 2018-05-25T12:32:30+02:00
Depends: libhtsjdk-java

- - - - -


8 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pilon (1.22+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at 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 +1,32 @@
+Source: pilon
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at 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
=====================================
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+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 at 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
=====================================
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+	dh $@


=====================================
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 +1,4 @@
+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)



View it on GitLab: https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e

-- 
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