[pkg-java] r17728 - in trunk/libjaba-client-java/debian: . bin patches
Timothy Booth
tbooth-guest at moszumanska.debian.org
Sun Feb 2 16:21:57 UTC 2014
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 <tbooth at ceh.ac.uk> 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 <fourmond at debian.org>
-Build-Depends: debhelper (>= 7.0.50~), javahelper, default-jdk,
- liblog4j1.2-java
-Standards-Version: 3.9.2
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+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 <fourmond at debian.org>
+Copyright: © 2008-2012 Tim Booth <tbooth at ceh.ac.uk>
+ 2011 Vincent Fourmond <fourmond at debian.org>
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
-- at 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
+
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