[med-svn] [varna] 01/01: initial debianization
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Feb 7 22:48:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository varna.
commit d41d8b9d68aa8d498ea3067d09043d2aac8c7d3e
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sun Feb 7 14:34:11 2016 -0800
initial debianization
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 26 ++++++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++++++++++++++
debian/javabuild | 1 +
debian/jlibs | 1 +
debian/manifest | 7 +++++++
debian/rules | 8 ++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 5 +++++
11 files changed, 94 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d68b226
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+varna (3-93+ds-1) UNRELEASED; urgency=medium
+
+ * Initial release. (Closes: #814050)
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sun, 07 Feb 2016 13:51:38 -0800
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..c145554
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: varna
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Build-Depends: debhelper (>= 9),
+ javahelper,
+ default-jdk
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/varna.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/varna.git
+Homepage: http://varna.lri.fr/
+
+Package: varna
+Architecture: all
+Depends: ${misc:Depends}
+Description: Visualization Applet for RNA
+ VARNA is Java lightweight Applet dedicated to drawing the secondary structure
+ of RNA. It is also a Swing component that can be very easily included in an
+ existing Java code working with RNA secondary structure to provide a fast and
+ interactive visualization.
+ .
+ Being free of fancy external library dependency and/or network access, the
+ VARNA Applet can be used as a base for a standalone applet. It looks
+ reasonably good and scales up or down nicely to adapt to the space available
+ on a web page, thanks to the anti-aliasing drawing primitives of Swing.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b988c51
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: VARNA
+Source: http://varna.lri.fr/index.php?lang=en&page=home&css=varna
+
+Files: *
+Copyright: © 2008 Kevin Darty, Alain Denise and Yann Ponty <Yann.Ponty at lri.fr>
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2016 Michael R. Crusoe <crusoe at ucdavis.edu>
+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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/javabuild b/debian/javabuild
new file mode 100644
index 0000000..855db0d
--- /dev/null
+++ b/debian/javabuild
@@ -0,0 +1 @@
+varna.jar VARNA.java fr
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..75bbd5e
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+varna.jar
diff --git a/debian/manifest b/debian/manifest
new file mode 100644
index 0000000..7d9f75f
--- /dev/null
+++ b/debian/manifest
@@ -0,0 +1,7 @@
+usr/share/java/varna.jar:
+ Main-Class: fr.orsay.lri.varna.applications.VARNAGUI
+ Application-Library-Allowable-Codebase: *
+ Application-Name: VARNA
+ Permissions: all-permissions
+ Caller-Allowable-Codebase: *
+ Codebase: *
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e37b55f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+DH_VERBOSE := 1
+JAVA_HOME=/usr/lib/jvm/default-java
+export JAVA_TOOL_OPTIONS=-Dfile.encoding=ISO-8859-1
+
+%:
+ dh $@ --with javahelper
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..b6bd444
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Darty, Kévin and Denise, Alain and Ponty, Yann
+ Title: "VARNA: Interactive drawing and editing of the RNA secondary structure"
+ Journal: Bioinformatics
+ Year: 2009
+ Volume: 25
+ Number: 15
+ Pages: 1974-1975
+ DOI: http://dx.doi.org/10.1093/bioinformatics/btp250
+ URL: http://bioinformatics.oxfordjournals.org/content/25/15/1974
+ eprint: http://bioinformatics.oxfordjournals.org/content/25/15/1974.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b27eeab
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+ opts="repacksuffix=+ds,dversionmangle=s/\+ds//g,compression=xz" \
+http://varna.lri.fr/index.php?page=downloads .*/VARNAv(.*)-src.jar
+
--
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