[med-svn] [sparta] 02/02: Added debian dir

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sparta.

commit bdc16979ba158b30f3595499933b05f1e256bbc6
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 29 14:53:14 2016 +0200

    Added debian dir
---
 debian/bin/sparta        |  3 +++
 debian/changelog         |  5 +++++
 debian/clean             |  1 +
 debian/compat            |  1 +
 debian/control           | 30 ++++++++++++++++++++++++++++++
 debian/copyright         | 14 ++++++++++++++
 debian/install           |  2 ++
 debian/rules             |  6 ++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 11 +++++++++++
 debian/watch             |  4 ++++
 11 files changed, 78 insertions(+)

diff --git a/debian/bin/sparta b/debian/bin/sparta
new file mode 100755
index 0000000..960e6a0
--- /dev/null
+++ b/debian/bin/sparta
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+python /usr/share/sparta/SPARTA.py $@
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..efc3c57
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sparta (1.01+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Thu, 28 Jul 2016 15:13:14 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..daa30a3
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+README.html
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..12ac5ba
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: sparta
+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 (>= 9),
+               python-all,
+               dh-python
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sparta.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/sparta.git
+Homepage: http://sparta.readthedocs.io/en/latest/
+
+Package: sparta
+Architecture: all
+Depends: ${python:Depends},
+         ${misc:Depends},
+         python-numpy,
+         default-jre,
+         r-base,
+         r-bioc-edger
+Description: automated reference-based bacterial RNA-seq Transcriptome Analysis
+ SPARTA is a workflow aimed at analyzing single-end Illumina RNA-seq
+ data. The workflow combines several tools: Trimmomatic (read
+ trimming/adapter removal), FastQC (read quality analysis), Bowtie
+ (mapping reads to the reference genome), HTSeq (transcript/gene feature
+ abundance counting), and edgeR (differential gene expression analysis).
+ Within the differential gene expression analysis step, batch effects can
+ be detected and the user is warned of the potential, unintended
+ additional variable. The analysis procedure is outlined below.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..93f1a61
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,14 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SPARTA
+Source: https://github.com/biobenkj/SPARTA_Linux/releases
+Files-Excluded: */DE_analysis
+                */Mapping_and_counting
+                */QC_analysis
+
+Files: *
+Copyright: 
+License: 
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: 
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..68b7786
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+*.py		usr/share/sparta
+debian/bin	usr
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..441c30d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@ --with python2
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..fdb4317
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+  Author: Benjamin K. Johnson and Matthew B. Scholz and Tracy K. Teal and Robert B. Abramovitch
+  Title: "SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis"
+  Journal: BMC Bioinformatics
+  Year: 2016
+  Volume: 17
+  Pages: 66
+  DOI: 10.1186/s12859-016-0923-y
+  PMID: 26847232
+  URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0923-y
+  eprint: http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0923-y
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1b4b054
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/biobenkj/SPARTA_Linux/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

-- 
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