[med-svn] [r-bioc-deseq2] 02/05: initial Debianization

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository r-bioc-deseq2.

commit 5cb1f886f1f209294526d81904f10f42486debcc
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 07:15:46 2016 -0800

    initial Debianization
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 29 +++++++++++++++++++++++++++++
 debian/copyright         | 13 +++++++++++++
 debian/examples          |  1 +
 debian/rules             |  4 ++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 9 files changed, 70 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f8a216f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-deseq2 (1.10.1-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #778586)
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu>  Mon, 16 Feb 2015 19:26:42 -0500
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..f7752ac
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: r-bioc-deseq2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               cdbs,
+               r-base-dev,
+               r-bioc-genefilter,
+               r-cran-ggplot2,
+               r-cran-hmisc,
+               r-cran-rcpparmadillo,
+               r-cran-foreign,
+               r-cran-nnet
+Standards-Version: 3.9.6
+Homepage: https://bioconductor.org/packages/DESeq2/
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/r-bioc-deseq2.git
+Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-deseq2.git
+
+Package: r-bioc-deseq2
+Architecture: any
+Depends: ${R:Depends},
+         ${misc:Depends},
+         ${shlibs:Depends}
+Description: R package for RNA-Seq Differential Expression Analysis
+ Differential gene expression analysis based on the negative binomial
+ distribution. Estimate variance-mean dependence in count data from
+ high-throughput sequencing assays and test for differential expression based
+ on a model using the negative binomial distribution.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..55f684a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,13 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: DESeq2
+Source: https://bioconductor.org/packages/DESeq2/
+
+Files: *
+Copyright: © 2014 Michael Love, Simon Anders, Wolfgang Huber
+License: LGPL-3.0+
+
+Files: debian/*
+Copyright: © 2016 Regents of the University of California
+License: LGPL-3.0+
+
+
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..18244c8
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+vignettes
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..aeb12b3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
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..1d97024
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Michael I Love and Wolfgang Huber and Simon Anders
+  Title: >
+    Moderated estimation of fold change and dispersion for {RNA}-seq data
+    with {DESeq}2
+  Journal: Genome Biol
+  Year: 2014
+  Volume: 15
+  Number: 12
+  DOI: http://dx.doi.org/10.1186/s13059-014-0550-8
+  URL: http://www.genomebiology.com/2014/15/12/550/abstract
+  eprint: http://www.genomebiology.com/2014/15/12/550
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b634835
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
+  http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html .*/DESeq2_([\d\.]+)\.tar\.gz

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