[med-svn] [nextsv] 01/01: Initial packaging (data only)

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository nextsv.

commit 644f9f2fef2155fc734e50598108779b0c9447ea
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Jan 5 00:37:50 2017 -0800

    Initial packaging (data only)
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 30 ++++++++++++++++++++++++++++++
 debian/copyright         | 21 +++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata |  7 +++++++
 6 files changed, 65 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f4f1945
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+nextsv (0.4.0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Afif Elghraoui <afif at debian.org>  Thu, 05 Jan 2017 00:31:56 -0800
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..6877699
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: nextsv
+Section: non-free/science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
+Build-Depends: debhelper (>= 10)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/nextsv.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/nextsv.git
+Homepage: https://github.com/Nextomics/nextsv
+
+Package: nextsv
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+	pbhoney,
+	sniffles,
+Description: automated structural variation detection for long-read sequencing
+ NextSV is an computational pipeline that allows structural variant (SV)
+ calling from PacBio sequencing data using PBhoney and Sniffles. NextSV takes
+ FASTA or FASTQ files as input. Once the SV caller is selected by user, NextSV
+ automatically chooses the compatible aligner and performs mapping. The
+ alignments will be automatically sorted and then presented to the SV caller.
+ Users can change the parameters by modifying its configuration file. When the
+ analysis is finished, NextSV will examine the FASTA/FASTQ, BAM, and result
+ files and generate a report showing various statistics. If more than both
+ callers are selected, NextSV will format the raw result files (.tails, .spots,
+ or .vcf files) into bed files and generate the intersection or union call set
+ for the purpose of higher accuracy or sensitivity.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..997fb19
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,21 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: NextSV
+Source: https://github.com/Nextomics/nextsv
+
+Files: *
+Copyright: © 2016 Grandomics Biosciences <support at grandomics.com>
+License: GB-nonfree
+ NextSV is freely available for academic use. It is provided without warranty
+ of any kind, including but not limited to the warranties of merchantability,
+ fitness for a particular purpose and non-infringement. No liability for the
+ software usage is assumed.
+ .
+ For commercial use please contact Grandomics Biosciences
+ (support at grandomics.com) for licensing options.
+Comment:
+ Pending license clarification at https://github.com/Nextomics/nextsv/issues/3
+ for redistributability and modifiability.
+
+Files: debian/*
+Copyright: © 2016 Afif Elghraoui <afif at debian.org>
+License: GPL-2.0+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..f040b8d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Reference:
+  Author: Li Fang and Jiang Hu and Depeng Wang and Kai Wang
+  Title: Evaluation on Detection of Structural Variants by Low-Coverage Long-Read Sequencing
+  Journal: bioRxiv
+  Year: 2016
+  DOI: 10.1101/092544
+  URL: https://doi.org/10.1101/092544

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