[med-svn] [gatk] 02/02: Initial packaging template
Andreas Tille
tille at debian.org
Thu Mar 26 12:39:11 UTC 2015
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tille pushed a commit to branch master
in repository gatk.
commit 1e0808a772d299ebd0f5c737bc79be8e21acde72
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 26 13:37:44 2015 +0100
Initial packaging template
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 22 ++++++++++++++++++++++
debian/copyright | 33 +++++++++++++++++++++++++++++++++
debian/createmanpages | 16 ++++++++++++++++
debian/doc-base | 20 ++++++++++++++++++++
debian/rules | 23 +++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 3 +++
10 files changed, 136 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b4a270e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+gatk (3.3-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 26 Mar 2015 13:20:02 +0100
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..48412a1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,22 @@
+Source: gatk
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/gatk.git
+Vcs-Git: git://anonscm.debian.org/debian-med/gatk.git
+Homepage: https://www.broadinstitute.org/gatk/
+
+Package: gatk
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: The Genome Analysis Toolkit
+ The Genome Analysis Toolkit or GATK is a software package developed at
+ the Broad Institute to analyze high-throughput sequencing data. The
+ toolkit offers a wide variety of tools, with a primary focus on variant
+ discovery and genotyping as well as strong emphasis on data quality
+ assurance. Its robust architecture, powerful processing engine and
+ high-performance computing features make it capable of taking on
+ projects of any size.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d4d4798
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,33 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GATK
+Source: https://github.com/broadgsa/gatk/
+
+Files: *
+Copyright: 2012-2014 The Broad Institute
+License: MIT
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..febcd91
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" <programname> > $MANDIR/<programname>.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..58ec00b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# 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))
+
+# alternatively to manually set those variables you can
+# include /usr/share/cdbs/1/rules/buildvars.mk
+# and use what is set there. Any hint whether dh might set variables in
+# a similar manner are welcome.
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
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..dbcdf29
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/broadgsa/gatk/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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