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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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.$1/g" \ -http://www.jalview.org/source jalview_([\d_]+)\.tar\.gz debian debian/new-upstream +http://www.jalview.org/source jalview_([\d_b]+)\.tar\.gz debian debian/new-upstream Modified: trunk/jalview/debian/wrappers/jalview =================================================================== --- trunk/jalview/debian/wrappers/jalview 2014-02-01 12:08:18 UTC (rev 17726) +++ trunk/jalview/debian/wrappers/jalview 2014-02-02 16:05:41 UTC (rev 17727) @@ -3,9 +3,16 @@ # Include the wrappers utility script . /usr/lib/java-wrappers/java-wrappers.sh -# We need openjdk or sun6 +# We need openjdk, preferably 7, or else sun6 +find_java_runtime openjdk7 >/dev/null 2>&1 find_java_runtime openjdk sun6 find_jar_classpath jalview +# Now if the user has no .jalview_properties, copy +# the default +if ! [ -e ~/.jalview_properties ] ; then + cp /etc/jalview_properties_default ~/.jalview_properties +fi + run_java jalview.bin.Jalview "$@" _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
