[med-svn] [r-hms-dbmi-spp] 01/04: initial Debianization

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository r-hms-dbmi-spp.

commit f6e58cd21162e779362e80c4a03bce36bca1ba44
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sat Oct 15 04:55:46 2016 -0700

    initial Debianization
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 29 +++++++++++++++++++++++++++++
 debian/copyright         | 11 +++++++++++
 debian/rules             | 21 +++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  3 +++
 8 files changed, 83 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ced574d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-hms-dbmi-spp (1.14-1) UNRELEASED; urgency=medium
+
+  * Initial release. (Closes: #XXXXXX)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sat, 15 Oct 2016 04:27:49 -0700
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..c91ef30
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: r-hms-dbmi-spp
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Build-Depends: debhelper (>= 9),
+               cdbs,
+               r-base-dev,
+               r-cran-catools,
+               libboost-dev,
+               r-bioc-rsamtools
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-cran-spp.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-spp.git
+Homepage: http://compbio.med.harvard.edu/Supplements/ChIP-seq/
+
+Package: r-hms-dbmi-spp
+Architecture: any
+Depends: ${R:Depends},
+         ${shlibs:Depends},
+         ${misc:Depends},
+         r-cran-catools,
+         r-bioc-rsamtools
+Description: GNU R package for processing ChIP-seq & other functional sequencing data
+ A set of routines for reading short sequence alignments, calculating tag
+ density, estimates of statistically significant enrichment/depletion
+ along the chromosome, identifying point binding positions (peaks), and
+ characterizing saturation properties related to sequencing depth.
+ 
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d991f5e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: spp
+Source: https://github.com/hms-dbmi/spp/releases
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: GPL-2
+
+Files: debian/*
+Copyright: © 2016 Michael R. Crusoe <michael.crusoe at gmail.com>
+License: GPL-2
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..803e2fe
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+export CXXFLAGS=-std=c++98
+
+debRreposname=hms-dbmi
+include /usr/share/R/debian/r-cran.mk
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG        := $(subst ~,_,$(VERSION))
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: 
+  Title: 
+  Journal: 
+  Year: 
+  Volume: 
+  Number: 
+  Pages: 
+  DOI: 
+  PMID:
+  URL: 
+  eprint: 
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1d40f89
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/hms-dbmi/spp/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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