Author: tbooth-guest Date: 2014-02-02 16:21:57 +0000 (Sun, 02 Feb 2014) New Revision: 17728
Added: trunk/libjaba-client-java/debian/README.Debian trunk/libjaba-client-java/debian/bin/ trunk/libjaba-client-java/debian/bin/jaba-client trunk/libjaba-client-java/debian/libjaba-client-java.install trunk/libjaba-client-java/debian/patches/make_services_public trunk/libjaba-client-java/debian/watch Removed: trunk/libjaba-client-java/debian/javabuild trunk/libjaba-client-java/debian/libjaba-client-java.dirs trunk/libjaba-client-java/debian/patches/strip-annotations.diff Modified: trunk/libjaba-client-java/debian/changelog trunk/libjaba-client-java/debian/control trunk/libjaba-client-java/debian/copyright trunk/libjaba-client-java/debian/libjaba-client-java.jlibs trunk/libjaba-client-java/debian/patches/series trunk/libjaba-client-java/debian/rules Log: New version of this library needed to build Jalview 2.8 Also added a little script to start the included GUI Added: trunk/libjaba-client-java/debian/README.Debian =================================================================== --- trunk/libjaba-client-java/debian/README.Debian (rev 0) +++ trunk/libjaba-client-java/debian/README.Debian 2014-02-02 16:21:57 UTC (rev 17728) @@ -0,0 +1,11 @@ +This package includes the basic client for JABAWS. + +To invoke the client you can run: + +$ java -jar /usr/share/java/jabaws.jar [args] + +Or more simply there is a convenience command: + +$ jabaws-client [args] + +Which does exactly the same thing. Added: trunk/libjaba-client-java/debian/bin/jaba-client =================================================================== --- trunk/libjaba-client-java/debian/bin/jaba-client (rev 0) +++ trunk/libjaba-client-java/debian/bin/jaba-client 2014-02-02 16:21:57 UTC (rev 17728) @@ -0,0 +1,7 @@ +#!/bin/sh + +# Run Varna, either launching the GUI or the VARNAcmd class depending +# on number of args. +JABAWSJAR=/usr/share/java/min-jaba-client.jar + +exec java -jar "$JABAWSJAR" "$@" Property changes on: trunk/libjaba-client-java/debian/bin/jaba-client ___________________________________________________________________ Added: svn:executable + * Modified: trunk/libjaba-client-java/debian/changelog =================================================================== --- trunk/libjaba-client-java/debian/changelog 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/changelog 2014-02-02 16:21:57 UTC (rev 17728) @@ -1,3 +1,12 @@ +libjaba-client-java (2.0.1-0biolinux3) precise; urgency=low + + * Updated package needed to build Jalview 2.8 + * Also provides a standalone scriptable client for JabaWS + in /usr/bin/jaba-client + * Ubuntu build + + -- Tim Booth <[email protected]> Wed, 08 Jan 2014 16:41:50 +0000 + libjaba-client-java (0+dfsg-1) unstable; urgency=low * Strip the *ThreadSafe class files from the source code, they are hardly Modified: trunk/libjaba-client-java/debian/control =================================================================== --- trunk/libjaba-client-java/debian/control 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/control 2014-02-02 16:21:57 UTC (rev 17728) @@ -2,19 +2,28 @@ Section: java Priority: optional Maintainer: Vincent Fourmond <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), javahelper, default-jdk, - liblog4j1.2-java -Standards-Version: 3.9.2 +Uploaders: Tim Booth <[email protected]> +Build-Depends: default-jdk, debhelper (>= 7.0.50~), javahelper, liblog4j1.2-java +Standards-Version: 3.9.3 Homepage: http://www.compbio.dundee.ac.uk/jabaws/ -Vcs-Svn: svn://svn.debian.org/svn/pkg-java/trunk/libjaba-client-java -Vcs-Browser: http://svn.debian.org/viewsvn/pkg-java/trunk/libjaba-client-java - Package: libjaba-client-java +Section: java Architecture: all Depends: ${misc:Depends}, ${java:Depends} -Description: minimal client for the JABAWS server - This package contains a library for building a client for the JABAWS - sequence alignment server. +Description: Client code for JabaWS server + JABAWS provides web services conveniently packaged to + run on your local computer, server, cluster or Amazon EC2 instance. Services + for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, + MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein + disorder with DisEMBL, IUPred, Jronn (a Java implementation of Ronn by P. + Troshin and G. Barton, unpublished) and GlobPlot; and calculation of amino acid + alignment conservation with AACon. . - This library is needed by jalview. + JABA 2.0.1 Web Services installations can be accessed from the Jalview desktop + application (version 2.8 onwards) and the JABAWS command-line client, and + provide multiple alignment and sequence analysis calculations limited only by + your own computing resources. + . + This package contains the command-line client plus the library code needed by + JalView. The server code is not yet packaged. Modified: trunk/libjaba-client-java/debian/copyright =================================================================== --- trunk/libjaba-client-java/debian/copyright 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/copyright 2014-02-02 16:21:57 UTC (rev 17728) @@ -1,43 +1,16 @@ -Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=174 -Upstream-Name: JABAWS command-line client -Source: http://www.compbio.dundee.ac.uk/jabaws/download.html - The "source" jar file actually found on that page is missing a few - bits, which were kindly provided privately by Peter Troshin. This - situation should improve soon enough. +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Files: * -Copyright: 2009, 2010 by Peter Troshin -License: Apache 2.0 - Licensed to the Apache Software Foundation (ASF) under one or more - contributor license agreements. See the NOTICE file distributed with - this work for additional information regarding copyright ownership. - The ASF licenses this file to You under the Apache License, Version 2.0 - (the "License"); you may not use this file except in compliance with - the License. You may obtain a copy of the License at - . - http://www.apache.org/licenses/LICENSE-2.0 - . - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. - . - On Debian system, the full text of the license can be found at - /usr/share/common-licenses/Apache-2.0 +Copyright: © 2009-2013 Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, + The Barton Group, University of Dundee, UK + © 2005 Brian Goetz and Tim Peierls +License: Apache-2.0 + On Debian systems, the complete text of the Apache-2.0 license + can be found in ‘/usr/share/common-licenses/Apache-2.0’. -Files: compbio/util/annotation/*ThreadSafe.java -Copyright: 2005 Brian Goetz and Tim Peierls -License: CC-BY - Released under the Creative Commons Attribution License - (http://creativecommons.org/licenses/by/2.5) - . - Any republication or derived work distributed in source code form - must include this copyright and license notice. - Files: debian/* -Copyright: 2011 by Vincent Fourmond <[email protected]> +Copyright: © 2008-2012 Tim Booth <[email protected]> + 2011 Vincent Fourmond <[email protected]> License: Apache 2.0 The debian packaging is licensed under the Apache 2.0 license, like most of the original code. - Deleted: trunk/libjaba-client-java/debian/javabuild =================================================================== --- trunk/libjaba-client-java/debian/javabuild 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/javabuild 2014-02-02 16:21:57 UTC (rev 17728) @@ -1 +0,0 @@ -min-jaba-client.jar src Deleted: trunk/libjaba-client-java/debian/libjaba-client-java.dirs =================================================================== --- trunk/libjaba-client-java/debian/libjaba-client-java.dirs 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/libjaba-client-java.dirs 2014-02-02 16:21:57 UTC (rev 17728) @@ -1 +0,0 @@ -usr/share/doc \ No newline at end of file Added: trunk/libjaba-client-java/debian/libjaba-client-java.install =================================================================== --- trunk/libjaba-client-java/debian/libjaba-client-java.install (rev 0) +++ trunk/libjaba-client-java/debian/libjaba-client-java.install 2014-02-02 16:21:57 UTC (rev 17728) @@ -0,0 +1 @@ +debian/bin/* /usr/bin Modified: trunk/libjaba-client-java/debian/libjaba-client-java.jlibs =================================================================== --- trunk/libjaba-client-java/debian/libjaba-client-java.jlibs 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/libjaba-client-java.jlibs 2014-02-02 16:21:57 UTC (rev 17728) @@ -1 +1 @@ -min-jaba-client.jar +*.jar Added: trunk/libjaba-client-java/debian/patches/make_services_public =================================================================== --- trunk/libjaba-client-java/debian/patches/make_services_public (rev 0) +++ trunk/libjaba-client-java/debian/patches/make_services_public 2014-02-02 16:21:57 UTC (rev 17728) @@ -0,0 +1,18 @@ +--- a/compbio/ws/client/Services.java ++++ b/compbio/ws/client/Services.java +@@ -39,7 +39,7 @@ + * Make sure this class has NO references to runners or engines as it is a + * part of minimal client package. Such things should go into ServicesUtil + */ +- MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS; ++ public MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS; + + public static Services getService(String servName) { + servName = servName.trim().toLowerCase(); +@@ -223,4 +223,4 @@ + public static void main(String[] args) { + System.out.println(MUSCLE_INFO); + } +-} +\ No newline at end of file ++} Modified: trunk/libjaba-client-java/debian/patches/series =================================================================== --- trunk/libjaba-client-java/debian/patches/series 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/patches/series 2014-02-02 16:21:57 UTC (rev 17728) @@ -1 +0,0 @@ -strip-annotations.diff Deleted: trunk/libjaba-client-java/debian/patches/strip-annotations.diff =================================================================== --- trunk/libjaba-client-java/debian/patches/strip-annotations.diff 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/patches/strip-annotations.diff 2014-02-02 16:21:57 UTC (rev 17728) @@ -1,20 +0,0 @@ -Index: libjaba-client-java-0+dfsg/compbio/metadata/RunnerConfig.java -=================================================================== ---- libjaba-client-java-0+dfsg.orig/compbio/metadata/RunnerConfig.java 2010-11-18 15:37:12.000000000 +0100 -+++ libjaba-client-java-0+dfsg/compbio/metadata/RunnerConfig.java 2011-10-22 09:06:15.465134107 +0200 -@@ -28,7 +28,6 @@ - import javax.xml.bind.annotation.XmlTransient; - - import compbio.util.SysPrefs; --import compbio.util.annotation.NotThreadSafe; - - /** - * The list of {@link Parameter}s and {@link Option}s supported by executable. -@@ -41,7 +40,6 @@ - * type of an Executable - */ - @XmlRootElement --@NotThreadSafe - public class RunnerConfig<T> { - - /* Modified: trunk/libjaba-client-java/debian/rules =================================================================== --- trunk/libjaba-client-java/debian/rules 2014-02-02 16:05:41 UTC (rev 17727) +++ trunk/libjaba-client-java/debian/rules 2014-02-02 16:21:57 UTC (rev 17728) @@ -6,12 +6,9 @@ %: dh $@ --with javahelper -override_dh_auto_clean: - rm -Rf src +override_jh_clean: + jh_clean + rm -f *.jar -override_dh_auto_build: - override_jh_build: - mkdir -p src; - cp -af compbio src/ - jh_build \ No newline at end of file + jh_build min-jaba-client.jar . Added: trunk/libjaba-client-java/debian/watch =================================================================== --- trunk/libjaba-client-java/debian/watch (rev 0) +++ trunk/libjaba-client-java/debian/watch 2014-02-02 16:21:57 UTC (rev 17728) @@ -0,0 +1,3 @@ +version=3 +# Download requires sign-up + _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
