[pkg-java] r17727 - in trunk/jalview/debian: . patches wrappers
Timothy Booth
tbooth-guest at moszumanska.debian.org
Sun Feb 2 16:05:42 UTC 2014
Author: tbooth-guest
Date: 2014-02-02 16:05:41 +0000 (Sun, 02 Feb 2014)
New Revision: 17727
Added:
trunk/jalview/debian/jalview.examples
trunk/jalview/debian/jalview_properties_default
trunk/jalview/debian/patches/newer-varna-api.diff
Modified:
trunk/jalview/debian/changelog
trunk/jalview/debian/control
trunk/jalview/debian/jalview.install
trunk/jalview/debian/new-upstream
trunk/jalview/debian/patches/mutilate-build-system.diff
trunk/jalview/debian/patches/newer-mime4j-api.diff
trunk/jalview/debian/patches/series
trunk/jalview/debian/rules
trunk/jalview/debian/watch
trunk/jalview/debian/wrappers/jalview
Log:
Jalview 2.8. Note new dependencies needed for this version will be committed soon.
This package was made on Ubuntu LTS so probably needs tweaking for Debian.
I added back some example data. As this comes from public databases and is not a
creative work it is public knowledge and thus not subject to licensing terms. Or
that's what I think. You may disagree.
Modified: trunk/jalview/debian/changelog
===================================================================
--- trunk/jalview/debian/changelog 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/changelog 2014-02-02 16:05:41 UTC (rev 17727)
@@ -1,3 +1,36 @@
+jalview (2.8.0b1.dfsg-0biolinux1) precise; urgency=low
+
+ * New minor release from upstream
+ * Re-jig patches but they are mostly the same
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sat, 01 Feb 2014 19:07:23 +0000
+
+jalview (2.8.dfsg-0biolinux4) precise; urgency=low
+
+ * Deb-Med sprint release
+ * Explicit JMOL version dependency
+ * Add default prefs file and link to local example rather than one
+ on the web
+ * Change new-upsream to preserve one demo file. All data in the file
+ public and factual (ie. not copyrightable)
+ * Modify watch file to see b releases (b=bugfix, not beta!)
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sat, 01 Feb 2014 16:45:55 +0000
+
+jalview (2.8.dfsg-0biolinux3) precise; urgency=low
+
+ * New upstream and backport for Ubuntu LTS/BL7
+ == 2.8.dfsg-0biolinux1
+ * Now needs JDAS, so I packaged that
+ * Also needs Varna, so I packaged that
+ * Generate properties file on build
+ * Depend on Spring-core
+ * Prefer JRE7 if available
+ * Fix link to JDAS library 1.x not 1.0.4
+ * Really use Java 7 if it is there.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sat, 01 Feb 2014 14:44:31 +0000
+
jalview (2.7.dfsg-4) UNRELEASED; urgency=low
* Removed the unused build dependency on libgnujaf-java
Modified: trunk/jalview/debian/control
===================================================================
--- trunk/jalview/debian/control 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/control 2014-02-02 16:05:41 UTC (rev 17727)
@@ -8,14 +8,15 @@
libaxis-java, libwsdl4j-java,
libgnumail-java, liblog4j1.2-java, javahelp2,
libcommons-discovery-java, libcommons-logging-java,
- libjmol-java (>= 12.1.42),
- jmol-applet (>= 12.1.42),
- libcastor-xml-java, libjaba-client-java,
+ libjmol-java (>= 12.2.2), libjmol-java (<= 13.0),
+ jmol-applet (>= 12.2.2),
+ libcastor-xml-java, libjaba-client-java (>=2.0.1),
javahelper, libjswingreader-java,
libmiglayout-java, icedtea-netx-common,
libhttpmime-java, libhttpcore-java,
libapache-mime4j-java (>= 0.7.2), libhttpclient-java,
- libvamsas-client-java
+ libvamsas-client-java, libjdas-java (>=1.0.2), libvarna-java,
+ libspring-core-java
Standards-Version: 3.9.5
Vcs-Svn: svn://anonscm.debian.org/pkg-java/trunk/jalview
Vcs-Browser: http://svn.debian.org/viewsvn/pkg-java/trunk/jalview
@@ -24,7 +25,7 @@
Package: jalview
Architecture: all
Depends: ${misc:Depends}, default-jre | java6-runtime,
- java-wrappers (>= 0.1.22), libjmol-java (>= 12.1.42), ${java:Depends}
+ java-wrappers (>= 0.1.22), libjmol-java (>= 12.2.1), ${java:Depends}
Suggests: kalign, t-coffee, clustalw
Description: multiple alignment editor
JalView is a Java alignment editor that can work with sequence
Added: trunk/jalview/debian/jalview.examples
===================================================================
--- trunk/jalview/debian/jalview.examples (rev 0)
+++ trunk/jalview/debian/jalview.examples 2014-02-02 16:05:41 UTC (rev 17727)
@@ -0,0 +1 @@
+exampleFile_2_7.jvp
Modified: trunk/jalview/debian/jalview.install
===================================================================
--- trunk/jalview/debian/jalview.install 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/jalview.install 2014-02-02 16:05:41 UTC (rev 17727)
@@ -1 +1,2 @@
-debian/wrappers/jalview usr/bin
\ No newline at end of file
+debian/wrappers/jalview usr/bin
+debian/jalview_properties_default etc
Added: trunk/jalview/debian/jalview_properties_default
===================================================================
--- trunk/jalview/debian/jalview_properties_default (rev 0)
+++ trunk/jalview/debian/jalview_properties_default 2014-02-02 16:05:41 UTC (rev 17727)
@@ -0,0 +1,2 @@
+#---JalviewX Properties File---
+STARTUP_FILE=/usr/share/doc/jalview/examples/exampleFile_2_7.jvp
Modified: trunk/jalview/debian/new-upstream
===================================================================
--- trunk/jalview/debian/new-upstream 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/new-upstream 2014-02-02 16:05:41 UTC (rev 17727)
@@ -28,6 +28,9 @@
# Removing the utils/ directory, not needed for build ?
rm -rf jalview*/utils
+#Save the examples jar from deletions
+( cd jalview*/examples && mv exampleFile_2_7.jar ../exampleFile_2_7.jvp )
+
# Removing all binary jars...
find -name '*.jar' | xargs rm
@@ -42,4 +45,4 @@
# We remove any file already existing there: it might be a symlink.
rm -f $orginame
mv $dir/$origname ..
-# rm -rf $dir
\ No newline at end of file
+# rm -rf $dir
Modified: trunk/jalview/debian/patches/mutilate-build-system.diff
===================================================================
--- trunk/jalview/debian/patches/mutilate-build-system.diff 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/patches/mutilate-build-system.diff 2014-02-02 16:05:41 UTC (rev 17727)
@@ -1,38 +1,52 @@
-Index: jalview-2.7.dfsg~almost/build.xml
-===================================================================
---- jalview-2.7.dfsg~almost.orig/build.xml 2011-09-27 16:50:20.000000000 +0200
-+++ jalview-2.7.dfsg~almost/build.xml 2011-10-16 00:25:56.823058139 +0200
-@@ -18,13 +18,6 @@
+--- a/build.xml
++++ b/build.xml
+@@ -18,14 +18,6 @@
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewX" default="usage" basedir=".">
- <!-- we use jalopy to format our sources -->
-- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-- <classpath>
-- <fileset dir="utils/jalopy/lib">
-- <include name="*.jar" />
-- </fileset>
-- </classpath>
-- </taskdef>
+- <!-- we use jalopy to format our sources -->
+- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+- <classpath>
+- <fileset dir="utils/jalopy/lib">
+- <include name="*.jar" />
+- </fileset>
+- </classpath>
+- </taskdef>
- <target name="help" depends="usage" />
- <target name="usage">
-@@ -114,10 +107,6 @@
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
-- <fileset dir="utils">
-- <include name="*.jar" />
-- <include name="**/*.jar" />
-- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
-@@ -407,7 +396,7 @@
- </axis-wsdl2java>
- </target>
+ <target name="help" depends="usage" />
+ <target name="usage">
+@@ -129,10 +121,6 @@
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+- <fileset dir="utils">
+- <include name="*.jar" />
+- <include name="**/*.jar" />
+- </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+@@ -172,18 +160,15 @@
+ </target>
-- <target name="makedist" depends="build, buildPropertiesFile, buildindices">
-+ <target name="makedist" depends="build, buildindices">
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
+
+- <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy" />
+ </tstamp>
+- <properties file="${outputDir}/.build_properties">
+- <header>
+- ---Jalview Build Details---
+- </header>
+- <property name="VERSION" value="${JALVIEW_VERSION}" />
+- <property name="BUILD_DATE" value="${build.date}" />
+- </properties>
++ <propertyfile file="${outputDir}/.build_properties"
++ comment="---Jalview Build Details---">
++ <entry key="VERSION" value="${JALVIEW_VERSION}" />
++ <entry key="BUILD_DATE" value="${build.date}" />
++ </propertyfile>
+ </target>
+
+
Modified: trunk/jalview/debian/patches/newer-mime4j-api.diff
===================================================================
--- trunk/jalview/debian/patches/newer-mime4j-api.diff 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/patches/newer-mime4j-api.diff 2014-02-02 16:05:41 UTC (rev 17727)
@@ -3,7 +3,7 @@
Forwarded: no
--- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
+++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
-@@ -26,9 +26,9 @@
+@@ -27,9 +27,9 @@
import java.util.List;
import org.apache.james.mime4j.MimeException;
@@ -14,4 +14,4 @@
+import org.apache.james.mime4j.stream.Field;
/**
- * ContentHandler for parsing mime encoded messages into Jalview objects.
+ * ContentHandler for parsing mime encoded messages into Jalview objects. TODO:
Added: trunk/jalview/debian/patches/newer-varna-api.diff
===================================================================
--- trunk/jalview/debian/patches/newer-varna-api.diff (rev 0)
+++ trunk/jalview/debian/patches/newer-varna-api.diff 2014-02-02 16:05:41 UTC (rev 17727)
@@ -0,0 +1,31 @@
+--- a/src/jalview/gui/AppVarna.java
++++ b/src/jalview/gui/AppVarna.java
+@@ -255,6 +255,12 @@
+ }
+
+ @Override
++ public void onTranslationChanged() {}
++
++ @Override
++ public void onZoomLevelChanged() {}
++
++ @Override
+ public void onWarningEmitted(String s)
+ {
+ // TODO Auto-generated method stub
+--- a/src/jalview/gui/AppVarnaBinding.java
++++ b/src/jalview/gui/AppVarnaBinding.java
+@@ -932,6 +932,13 @@
+ // TODO Auto-generated method stub
+
+ }
++
++ @Override
++ public void onTranslationChanged() {}
++
++ @Override
++ public void onZoomLevelChanged() {}
++
+ }
+
+ /*
Modified: trunk/jalview/debian/patches/series
===================================================================
--- trunk/jalview/debian/patches/series 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/patches/series 2014-02-02 16:05:41 UTC (rev 17727)
@@ -1,3 +1,3 @@
mutilate-build-system.diff
-newer-jmol-api.diff
newer-mime4j-api.diff
+newer-varna-api.diff
Modified: trunk/jalview/debian/rules
===================================================================
--- trunk/jalview/debian/rules 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/rules 2014-02-02 16:05:41 UTC (rev 17727)
@@ -21,8 +21,11 @@
castor-core Jmol min-jaba-client axis-jaxrpc commons-discovery \
axis jh vamsas-client /usr/share/jmol-applet/JmolApplet.jar \
jswingreader miglayout /usr/share/icedtea-web/plugin.jar \
- httpmime httpcore apache-mime4j-core httpclient jsearch-indexer
+ httpmime httpcore apache-mime4j-core httpclient jsearch-indexer \
+ /usr/share/maven-repo/uk/ac/ebi/das/jdas/1.x/jdas-1.x.jar \
+ varna jackson-core-lgpl spring3-core-3.x
+DEB_COMPRESS_EXCLUDE_ALL=.jvp
ANT_OPTS := -Dbuild.sysclasspath=last \
-DJALVIEW_VERSION=$(VERSION)
Modified: trunk/jalview/debian/watch
===================================================================
--- trunk/jalview/debian/watch 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/watch 2014-02-02 16:05:41 UTC (rev 17727)
@@ -1,3 +1,3 @@
version=3
opts="dversionmangle=s/\.dfsg//,uversionmangle=s/_/./g;s/\.0(\d)/.0.$1/g" \
-http://www.jalview.org/source jalview_([\d_]+)\.tar\.gz debian debian/new-upstream
+http://www.jalview.org/source jalview_([\d_b]+)\.tar\.gz debian debian/new-upstream
Modified: trunk/jalview/debian/wrappers/jalview
===================================================================
--- trunk/jalview/debian/wrappers/jalview 2014-02-01 12:08:18 UTC (rev 17726)
+++ trunk/jalview/debian/wrappers/jalview 2014-02-02 16:05:41 UTC (rev 17727)
@@ -3,9 +3,16 @@
# Include the wrappers utility script
. /usr/lib/java-wrappers/java-wrappers.sh
-# We need openjdk or sun6
+# We need openjdk, preferably 7, or else sun6
+find_java_runtime openjdk7 >/dev/null 2>&1
find_java_runtime openjdk sun6
find_jar_classpath jalview
+# Now if the user has no .jalview_properties, copy
+# the default
+if ! [ -e ~/.jalview_properties ] ; then
+ cp /etc/jalview_properties_default ~/.jalview_properties
+fi
+
run_java jalview.bin.Jalview "$@"
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