biology/jalview: Update 2.07 -> 2.11.1.4
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This commit is contained in:
Yuri Victorovich
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d8cfb1d029
commit
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@ -1,27 +1,73 @@
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# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
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PORTNAME= jalview
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PORTVERSION= 2.07
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PORTREVISION= 3
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DISTVERSION= 2.11.1.4
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CATEGORIES= biology java
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MASTER_SITES= http://www.jalview.org/source/
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DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/}
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MASTER_SITES= https://www.jalview.org/source/
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DISTNAME= ${PORTNAME}_${DISTVERSION:S/./_/g}
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DISTFILES= ${DISTNAME}${EXTRACT_SUFX}
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EXTRACT_ONLY= ${PORTNAME}_${DISTVERSION:S/./_/g}${EXTRACT_SUFX}
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MAINTAINER= ports@FreeBSD.org
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EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Viewer and editor for multiple sequence alignments
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKSRC}/LICENSE
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BUILD_DEPENDS= gradle:devel/gradle
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USE_JAVA= yes
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JAVA_VERSION= 8
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USE_ANT= yes
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ALL_TARGET= makejars
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JAVA_VERSION= 11
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WRKSRC= ${WRKDIR}/${PORTNAME}
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USE_LOCALE= en_US.UTF-8
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DATADIR= ${JAVASHAREDIR}/${PORTNAME}
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SUB_FILES= jalview.sh
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SUB_LIST= JAVA=${JAVA}
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NO_ARCH= yes
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# to rebuild the deps archive:
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# 1. set DEV_UPDATE_MODE=yes
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# 2. make makesum build
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# 3. upload the *-deps archive
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# 4. set DEV_UPDATE_MODE=no
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# 5. make clean makesum
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DEV_UPDATE_MODE= no
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DEPS_CACHE_DIR= ${WRKDIR}
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.if (${DEV_UPDATE_MODE} == "yes")
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post-build:
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@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
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@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
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.else
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MASTER_SITES+= LOCAL/yuri/:deps
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DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
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GRADLE_ARGS= --offline
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post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven
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@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
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.endif
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BINARY_ALIAS= git=false java=${JAVA}
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PLIST_FILES= bin/jalview \
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${DATADIR}/jalview.jar
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do-build:
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@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
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--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
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${GRADLE_ARGS} --build-cache shadowJar
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do-install:
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${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${STAGEDIR}${PREFIX}/bin/jalview
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@${MKDIR} ${STAGEDIR}${DATADIR}
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${INSTALL_DATA} ${WRKSRC}/dist/* ${STAGEDIR}${DATADIR}
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${INSTALL_DATA} ${WRKSRC}/build/libs/jalview-all-${DISTVERSION}-j${JAVA_VERSION}.jar ${STAGEDIR}${DATADIR}/jalview.jar
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.include <bsd.port.mk>
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@ -1,2 +1,5 @@
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SHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7
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SIZE (jalview_2_07.tar.gz) = 8439780
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TIMESTAMP = 1619390838
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SHA256 (jalview_2_11_1_4.tar.gz) = 30c0a89bbaf58bc5fd15fd7b167768d21cda1431676f28e22669fd5a342396eb
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SIZE (jalview_2_11_1_4.tar.gz) = 103154170
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SHA256 (jalview-2.11.1.4-deps.tar.gz) = 93e88557841d295146aa5f9144e22a8774c9699c9a6a43a4a25673148d91c7d9
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SIZE (jalview-2.11.1.4-deps.tar.gz) = 21061379
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@ -1,4 +1,3 @@
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#!/bin/sh
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# Shell script to launch jalview using our javavm wrapper
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"%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview
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%%JAVA%% -classpath %%DATADIR%% -jar %%DATADIR%%/jalview.jar jalview.bin.Jalview
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@ -1,50 +0,0 @@
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This patch removes the webstart support.
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--- build.xml.orig Mon Dec 12 14:57:02 2005
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+++ build.xml Fri Jan 27 12:20:52 2006
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@@ -180,6 +180,10 @@
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</fileset>
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</copy>
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<!-- the default keystore details might need to be edited here -->
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+<!-- Remove all the remaining stuff for this target
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+ which is only necessary if we want to start jalview
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+ using java web start. It requires us to generate a key
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+ before building the port - Fernan - 27.Jan.2006
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<signjar
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storepass="alignmentisfun"
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keypass="alignmentisfun"
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@@ -194,8 +198,9 @@
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</fileset>
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</signjar>
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<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
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-
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+-->
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<!-- codebase="http://www.jalview.org/jalview/webstart" -->
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+<!--
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<jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
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codebase="${WebStartLocation}">
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<information>
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@@ -206,6 +211,7 @@
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<description kind="short">Jalview</description>
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<icon href="logo_big.gif"/>
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<offline_allowed/>
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+-->
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<!--
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<association mime-type="application-x/ext-file" extensions="fa"/>
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<association mime-type="application-x/ext-file" extensions="fasta"/>
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@@ -216,6 +222,7 @@
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<association mime-type="application-x/ext-file" extensions="aln"/>
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<association mime-type="application-x/ext-file" extensions="pir"/>
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-->
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+<!--
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</information>
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<resources>
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<j2se version="1.4+"/>
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@@ -234,6 +241,7 @@
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<all_permissions/>
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</security>
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</jnlp>
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+-->
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</target>
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<target name="runenv" depends="init">
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<path id="run.classpath">
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@ -22,4 +22,4 @@ o Output alignments as HTML pages, images (PNG) or postscript (EPS).
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If you use Jalview in your work, please quote this publication. Clamp, M., et
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al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7
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WWW: http://www.jalview.org
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WWW: https://www.jalview.org
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@ -1,16 +0,0 @@
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bin/jalview
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%%DATADIR%%/activation.jar
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%%DATADIR%%/xercesImpl.jar
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%%DATADIR%%/wsdl4j.jar
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%%DATADIR%%/saaj.jar
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%%DATADIR%%/regex.jar
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%%DATADIR%%/mail.jar
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%%DATADIR%%/log4j-1.2.8.jar
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%%DATADIR%%/jhall.jar
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%%DATADIR%%/jaxrpc.jar
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%%DATADIR%%/jalview.jar
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%%DATADIR%%/commons-logging.jar
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%%DATADIR%%/commons-discovery.jar
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%%DATADIR%%/castor-0.9.6-xml.jar
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%%DATADIR%%/axis.jar
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%%DATADIR%%/xml-apis.jar
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