[pkg-java] r17733 - in trunk/varna: . debian debian/bin debian/source
Timothy Booth
tbooth-guest at moszumanska.debian.org
Sun Feb 2 16:54:49 UTC 2014
Author: tbooth-guest
Date: 2014-02-02 16:54:49 +0000 (Sun, 02 Feb 2014)
New Revision: 17733
Added:
trunk/varna/debian/
trunk/varna/debian/README.Debian
trunk/varna/debian/bin/
trunk/varna/debian/bin/varna
trunk/varna/debian/changelog
trunk/varna/debian/compat
trunk/varna/debian/control
trunk/varna/debian/copyright
trunk/varna/debian/libvarna-java.examples
trunk/varna/debian/libvarna-java.install
trunk/varna/debian/libvarna-java.jlibs
trunk/varna/debian/libvarna-java.manifest
trunk/varna/debian/rules
trunk/varna/debian/source/
trunk/varna/debian/source/format
trunk/varna/debian/varna.1.pod
trunk/varna/debian/varna.manpages
trunk/varna/debian/watch
Log:
Library needed for newer Jalview but also generally useful.
Build was done on Ubuntu 12.04 but should be good for Debian too.
Added: trunk/varna/debian/README.Debian
===================================================================
--- trunk/varna/debian/README.Debian (rev 0)
+++ trunk/varna/debian/README.Debian 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,38 @@
+TODO - make this into a manpage for the varna script.
+
+VARNA is a tool for the automated drawing, visualization and annotation of the
+secondary structure of RNA, designed as a companion software for web servers
+and databases.
+Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
+electronic mail : Yann.Ponty at lri.fr
+paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
+
+The latest version of this software can be found at:
+ http://varna.lri.fr
+
+%%%%%%%%%%%%%%%%%%%%%%%%% INVOKING THE GUI VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+A basic editor demonstrating the features of VARNA can be spawned by running the
+"varna" command, which actually runs:
+
+java -jar /usr/share/java/varna.jar applis.VARNAGUI
+
+%%%%%%%%%%%%%%%%%%%%%% INVOKING COMMAND LINE VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+VARNA can also be used as a standalone application for producing pictures. If any
+arguments are supplied to varna then the VARNAcmd class will be invoked. It
+can be used as follows:
+
+ varna [-i inputFile|-sequenceDBN XXX -structureDBN YYY] -o outFile [opts]
+
+Where:
+ * inFile: An input file using one of the supported formats (Vienna, CT, BPSeq or RNAML).
+ * XXX: An RNA sequence.
+ * YYY: A dot-bracket representation of this RNA.
+ * outFile: An output file whose format is guessed from the extension.
+
+Many additional options are supported, matching the syntax of the Applet's parameters.
+Namely, if param is a valid parameter for the VARNA Applet, then -param is an option
+that has the exact same arguments and effects in the standalone, command-line version.
+
+Use varna -h or varna -x for help.
Added: trunk/varna/debian/bin/varna
===================================================================
--- trunk/varna/debian/bin/varna (rev 0)
+++ trunk/varna/debian/bin/varna 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+# Run Varna, either launching the GUI or the VARNAcmd class depending
+# on number of args.
+VJAR=/usr/share/java/varna.jar
+
+if [ "$#" = 0 ] ; then
+ exec java -jar "$VJAR" applis.VARNAGUI
+else
+ exec java -cp "$VJAR" fr.orsay.lri.varna.applications.VARNAcmd "$@"
+fi
Property changes on: trunk/varna/debian/bin/varna
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/varna/debian/changelog
===================================================================
--- trunk/varna/debian/changelog (rev 0)
+++ trunk/varna/debian/changelog 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,9 @@
+varna (3.9-0biolinux2) precise; urgency=low
+
+ * Package built and tested on Ubunto 12.04LTS
+ * New package needed by Jalview
+ * Added a /usr/bin/varna convenience script.
+ * Made a manpage for this from the output of varna -h and varna -x
+ * Nice minimal rules using jh_build
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 10 Jan 2014 12:44:33 +0000
Added: trunk/varna/debian/compat
===================================================================
--- trunk/varna/debian/compat (rev 0)
+++ trunk/varna/debian/compat 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1 @@
+7
Added: trunk/varna/debian/control
===================================================================
--- trunk/varna/debian/control (rev 0)
+++ trunk/varna/debian/control 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,27 @@
+Source: varna
+Section: java
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: default-jdk, testng, debhelper (>= 7.0.50~), javahelper
+Standards-Version: 3.9.3
+Homepage: http://varna.lri.fr
+
+Package: libvarna-java
+Section: java
+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.
+ .
+ Please cite:
+ VARNA: Interactive drawing and editing of the RNA secondary structure
+ Kévin Darty, Alain Denise and Yann Ponty
+ Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009
Added: trunk/varna/debian/copyright
===================================================================
--- trunk/varna/debian/copyright (rev 0)
+++ trunk/varna/debian/copyright 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,20 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+
+Files: *
+Copyright: © 2008-2012 Kevin Darty, Alain Denise, Yann Ponty
+License: GPL-3
+ VARNA 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.
+
+ VARNA version 3.1 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, the complete text of the GNU General Public License version
+ 3 can be found in ‘/usr/share/common-licenses/GPL-3’.
+
+Files: debian/*
+Copyright: © 2008-2012 Tim Booth
+License: GPL-3
Added: trunk/varna/debian/libvarna-java.examples
===================================================================
--- trunk/varna/debian/libvarna-java.examples (rev 0)
+++ trunk/varna/debian/libvarna-java.examples 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1 @@
+VARNA.js
Added: trunk/varna/debian/libvarna-java.install
===================================================================
--- trunk/varna/debian/libvarna-java.install (rev 0)
+++ trunk/varna/debian/libvarna-java.install 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,2 @@
+*.jar /usr/share/java
+debian/bin/* /usr/bin
Added: trunk/varna/debian/libvarna-java.jlibs
===================================================================
--- trunk/varna/debian/libvarna-java.jlibs (rev 0)
+++ trunk/varna/debian/libvarna-java.jlibs 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1 @@
+*.jar
Added: trunk/varna/debian/libvarna-java.manifest
===================================================================
--- trunk/varna/debian/libvarna-java.manifest (rev 0)
+++ trunk/varna/debian/libvarna-java.manifest 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,7 @@
+usr/share/java/varna.jar:
+ Manifest-Version: 1.0
+ Application-Name: VARNA
+ Permissions: all-permissions
+ Created-By: Ninja Badgers
+ Implementation-Vendor: Yann Ponty
+ Main-Class: fr.orsay.lri.varna.applications.VARNAGUI
Added: trunk/varna/debian/rules
===================================================================
--- trunk/varna/debian/rules (rev 0)
+++ trunk/varna/debian/rules 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+ dh $@ --with javahelper
+
+override_jh_build:
+ jh_build varna.jar .
+ jar uf varna.jar *.dtd
+ debian/varna.1.pod
+
+override_jh_clean:
+ jh_clean
+ rm -f *.jar
+ rm -f *.1
+
+# I did this before realising jh_build does it all for me...
+# SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+#
+# override_dh_auto_clean:
+# find -name '*.class' -delete
+# rm -f *.jar
+#
+# override_dh_auto_build:
+# #Some files seem to contain both UTF and ASCII so ignore the
+# #warnings about illegal characters in comments.
+# find fr -name '*.java' | javac @/dev/stdin
+# javac *.java
+# find fr rnaml.dtd *.class -type f -not -name '*.java' |\
+# jar cvf varna-$(SRC_VERSION).jar @/dev/stdin
+# ln -s varna-$(SRC_VERSION).jar varna.jar
+
Property changes on: trunk/varna/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/varna/debian/source/format
===================================================================
--- trunk/varna/debian/source/format (rev 0)
+++ trunk/varna/debian/source/format 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/varna/debian/varna.1.pod
===================================================================
--- trunk/varna/debian/varna.1.pod (rev 0)
+++ trunk/varna/debian/varna.1.pod 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,125 @@
+#!/bin/bash
+echo pod2man --utf8 -c 'VARNA Wrapper' "$0" ">" `basename "$0" .pod`
+exec pod2man --utf8 -c 'VARNA Wrapper' "$0" > `basename "$0" .pod`
+
+=encoding utf8
+
+=head1 NAME
+
+VARNA - Visualization Applet for RNA
+
+=head1 VERSION
+
+This documentation refers to version 3.9
+
+=head1 SYNOPSIS
+
+Run the Varna simple GUI
+
+ varna
+
+Create an image on the command line
+
+ varna [-i InFile|-sequenceDBN XXX -structureDBN YYY] -o OutFile [Options]
+
+=head1 DESCRIPTION
+
+B<Basic usage:>
+The varna command on Debian is a simple convenience wrapper to invoke the VARNA JAR file.
+When run with no paramenters, the Java GUI will be launched to view RNA structures interactively.
+
+To create an image on the command line, use the -i and -o options to specify the file to convert
+and the file to produce, where:
+ -o OutFile Supported formats: {JPEG,PNG,EPS,XFIG,SVG}
+ -i InFile Secondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}
+
+B<Main options:>
+ -algorithm Drawing algorithm, choosen from [naview,line,radiate,circular]
+ -backbone Backbone color (Ex: #334455)
+ -baseInner Default value for inner base color (Ex: #334455)
+ -baseOutline Base outline color (Ex: #334455)
+ -bp Base pair color (Ex: #334455)
+ -bpStyle Look and feel for base pairs drawings, choosen from [lw,none,simple,rnaviz]
+ -h Displays a short description of main options and exits
+ -periodNum Periodicity of base-numbering
+ -x Displays a detailed description of all options
+
+B<Advanced options:>
+ -annotations A set of textual annotations
+ -applyBasesStyle Base style application
+ -autoHelices
+ -autoInteriorLoops
+ -autoTerminalLoops
+ -auxBPs Adds a list of (possibly non-canonical) base-pairs to those already defined by
+ the main secondary structure (Ex: "(1,10);(2,11);(3,12)"). Custom BP styles
+ can be specified (Ex: "(2,11):thickness=4;(3,12):color=#FF0000").
+ -background Background color (Ex: #334455)
+ -baseName Residues font color (Ex: #334455)
+ -baseNum Base numbers font color (Ex: #334455)
+ -basesStyle Base style declaration
+ -border Border width and height in pixels (Ex: "20x40")
+ -bpIncrement Distance between nested base-pairs (i.e. arcs) in linear representation
+ -chemProb
+ -colorMap Associates a list of numerical values (eg '0.2,0.4,0.6,0.8') with the RNA base
+ s with respect to their natural order, and modifies the color used to fill the
+ se bases according to current color map style.
+ -colorMapCaption Sets current color map caption.
+ -colorMapMax
+ -colorMapMin
+ -colorMapStyle Selects a specific color map style. It can be either one of the predefined
+ styles (eg 'red', 'green', 'blue', 'bw', 'heat', 'energy') or a new one
+ (eg '0:#FFFF00;1:#ffFFFF;6:#FF0000').
+ -columns
+ -comparisonMode Activates comparison mode
+ -customBPs
+ -customBases
+ -drawBackbone True if the backbone must be drawn, false otherwise
+ -drawBases Shows/hide the outline of bases
+ -drawColorMap
+ -drawNC Toggles on/off display of non-canonical base-pairs
+ -drawTertiary Toggles on/off display of tertiary interaction, ie pseudoknots
+ -error Show errors
+ -fillBases Fills or leaves empty the inner portions of bases
+ -firstSequence In comparison mode, sequence of first RNA
+ -firstStructure In comparison mode, structure of first RNA
+ -flat Toggles on/off (true/false) drawing exterior bases on a straight line
+ -gapsColor Define and use custom color for gaps bases in comparison mode
+ -highlightRegion
+ -modifiable Allows/prohibits modifications
+ -nsBasesColor Define and use custom color for non-standard bases in comparison mode
+ -orientation Sets the general orientation of an RNA, i.e. the deviation of the longest axis
+ (defined by the most distant couple of bases) from the horizontal axis.
+ -quality Sets quality (non-vector file formats only)
+ -resolution Sets resolution (non-vector file formats only)
+ -rotation Rotates RNA after initial drawing (Ex: '20' for a 20 degree counter-clockwise
+ rotation)
+ -rows
+ -secondSequence In comparison mode, sequence of second RNA
+ -secondStructure In comparison mode, structure of second RNA
+ -sequenceDBN Raw RNA sequence
+ -spaceBetweenBases Sets the space between consecutive bases
+ -structureDBN RNA structure given in dot bracket notation (DBN)
+ -title RNA drawing title
+ -titleColor Title color (Ex: #334455)
+ -titleSize Title font size
+ -warning Show warnings
+ -zoom Zoom coefficient
+ -zoomAmount Zoom increment on user interaction
+
+=head1 AUTHOR
+
+ Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
+ e-mail : Yann.Ponty at lri.fr
+ paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
+
+More info and latest version of this software can be found at:
+ http://varna.lri.fr
+
+=head1 LICENCE AND COPYRIGHT
+
+ VARNA is free software.
+
+ see /usr/share/doc/libvarna-java/copyright
+
+=cut
+
Property changes on: trunk/varna/debian/varna.1.pod
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/varna/debian/varna.manpages
===================================================================
--- trunk/varna/debian/varna.manpages (rev 0)
+++ trunk/varna/debian/varna.manpages 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1 @@
+varna.1
Added: trunk/varna/debian/watch
===================================================================
--- trunk/varna/debian/watch (rev 0)
+++ trunk/varna/debian/watch 2014-02-02 16:54:49 UTC (rev 17733)
@@ -0,0 +1,3 @@
+version=3
+opts="uversionmangle=s/-/./g" http://varna.lri.fr/bin/VARNAv([0-9.-]+)-src.jar
+
More information about the pkg-java-commits
mailing list