[med-svn] [brig] 02/02: Initial Debian packaging

Fri Nov 27 07:42:43 UTC 2015

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tille pushed a commit to branch master
in repository brig.

commit f5c043167b9dacb02379a37505a1a97093ad350a
Author: Andreas Tille <tille at debian.org>
Date:   Fri Nov 27 08:41:20 2015 +0100

    Initial Debian packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 36 ++++++++++++++++++++++++++++++++++++
 debian/copyright         | 28 ++++++++++++++++++++++++++++
 debian/rules             | 22 ++++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 8 files changed, 109 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2a147cb
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+brig (0.95+dfsg-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 27 Nov 2015 08:36:19 +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..c01e94e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,36 @@
+Source: brig
+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),
+               javahelper,
+               libbatik-java,
+               libcommons-lang-java,
+               libjargs-java,
+               libxerces2-java
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/brig.git
+Vcs-Git: git://anonscm.debian.org/debian-med/brig.git
+Homepage: http://sourceforge.net/projects/brig/
+
+Package: brig
+Architecture: any
+Depends: ${java:Depends},
+         ${misc:Depends}
+Description: BLAST Ring Image Generator
+ BRIG can display circular comparisons between a large number of genomes,
+ with a focus on handling genome assembly data.
+  * Images show similarity between a central reference sequence and other
+    sequences as concentric rings.
+  * BRIG will perform all BLAST comparisons and file parsing automatically
+    via a simple GUI.
+  * Contig boundaries and read coverage can be displayed for draft genomes;
+    customized graphs and annotations can be displayed.
+  * Using a user-defined set of genes as input, BRIG can display gene
+    presence, absence, truncation or sequence variation in a set of
+    complete genomes, draft genomes or even raw, unassembled sequence data.
+  * BRIG also accepts SAM-formatted read-mapping files enabling genomic
+    regions present in unassembled sequence data from multiple samples to
+    be compared simultaneously
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..53bacb7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BRIG
+Source: http://sourceforge.net/projects/brig/files
+Files-Excluded: */*.jar
+                */.DS_Store
+                *.pdf
+
+Files: *
+Copyright: 2010-2012 Nabil Alikhan 
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+ .
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7a8ee54
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/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/dpkg/default.mk
+# and use what is set there.
+
+%:
+	dh $@
+
+get-orig-source:
+	uscan --verbose --force-download --repack --compression xz
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..44a47ae
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+   http://sf.net/brig/BRIG-(\d[\d\.]+)-dist\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)

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