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 : [email protected] +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 <[email protected]> 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 <[email protected]> +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 : [email protected] + 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 + _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
