biology/jalview: Update 2.07 -> 2.11.1.4

Take maintainership.

6 files changed, 62 insertions, 80 deletions

diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile
index 33341bd764c1..f99bd8d81676 100644
--- a/biology/jalview/Makefile
+++ b/biology/jalview/Makefile
@@ -1,27 +1,73 @@
 # Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
 
 PORTNAME=	jalview
-PORTVERSION=	2.07
-PORTREVISION=	3
+DISTVERSION=	2.11.1.4
 CATEGORIES=	biology java
-MASTER_SITES=	http://www.jalview.org/source/
-DISTNAME=	${PORTNAME}_${PORTVERSION:S/./_/}
+MASTER_SITES=	https://www.jalview.org/source/
+DISTNAME=	${PORTNAME}_${DISTVERSION:S/./_/g}
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
+EXTRACT_ONLY=	${PORTNAME}_${DISTVERSION:S/./_/g}${EXTRACT_SUFX}
 
-MAINTAINER=	ports@FreeBSD.org
+EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
+
+MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Viewer and editor for multiple sequence alignments
 
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	gradle:devel/gradle
+
 USE_JAVA=	yes
-JAVA_VERSION=	8
-USE_ANT=	yes
-ALL_TARGET=	makejars
+JAVA_VERSION=	11
+
 WRKSRC=		${WRKDIR}/${PORTNAME}
 
+USE_LOCALE=	en_US.UTF-8
+
 DATADIR=	${JAVASHAREDIR}/${PORTNAME}
 SUB_FILES=	jalview.sh
+SUB_LIST=	JAVA=${JAVA}
+
+NO_ARCH=	yes
+
+# to rebuild the deps archive:
+#   1. set DEV_UPDATE_MODE=yes
+#   2. make makesum build
+#   3. upload the *-deps archive
+#   4. set DEV_UPDATE_MODE=no
+#   5. make clean makesum
+
+DEV_UPDATE_MODE=	no
+
+DEPS_CACHE_DIR= ${WRKDIR}
+
+.if (${DEV_UPDATE_MODE} == "yes")
+post-build:
+	@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
+	@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
+.else
+MASTER_SITES+=	LOCAL/yuri/:deps
+DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
+GRADLE_ARGS=	--offline
+
+post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven
+	@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
+.endif
+
+BINARY_ALIAS=	git=false java=${JAVA}
+
+PLIST_FILES=	bin/jalview \
+		${DATADIR}/jalview.jar
+
+do-build:
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
+		--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
+		${GRADLE_ARGS} --build-cache shadowJar
 
 do-install:
 	${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${STAGEDIR}${PREFIX}/bin/jalview
 	@${MKDIR} ${STAGEDIR}${DATADIR}
-	${INSTALL_DATA} ${WRKSRC}/dist/* ${STAGEDIR}${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/build/libs/jalview-all-${DISTVERSION}-j${JAVA_VERSION}.jar ${STAGEDIR}${DATADIR}/jalview.jar
 
 .include <bsd.port.mk>
diff --git a/biology/jalview/distinfo b/biology/jalview/distinfo
index a92579a7f909..1a5fba7ea4d9 100644
--- a/biology/jalview/distinfo
+++ b/biology/jalview/distinfo
@@ -1,2 +1,5 @@
-SHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7
-SIZE (jalview_2_07.tar.gz) = 8439780
+TIMESTAMP = 1619390838
+SHA256 (jalview_2_11_1_4.tar.gz) = 30c0a89bbaf58bc5fd15fd7b167768d21cda1431676f28e22669fd5a342396eb
+SIZE (jalview_2_11_1_4.tar.gz) = 103154170
+SHA256 (jalview-2.11.1.4-deps.tar.gz) = 93e88557841d295146aa5f9144e22a8774c9699c9a6a43a4a25673148d91c7d9
+SIZE (jalview-2.11.1.4-deps.tar.gz) = 21061379
diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in
index 33b1a7e75195..eb25b886f2de 100644
--- a/biology/jalview/files/jalview.sh.in
+++ b/biology/jalview/files/jalview.sh.in
@@ -1,4 +1,3 @@
 #!/bin/sh
-# Shell script to launch jalview using our javavm wrapper
 
-"%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview
+%%JAVA%% -classpath %%DATADIR%% -jar %%DATADIR%%/jalview.jar jalview.bin.Jalview
diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml
deleted file mode 100644
index 7d6449347ba4..000000000000
--- a/biology/jalview/files/patch-build.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-This patch removes the webstart support.
-
---- build.xml.orig	Mon Dec 12 14:57:02 2005
-+++ build.xml	Fri Jan 27 12:20:52 2006
-@@ -180,6 +180,10 @@
-         </fileset>
-       </copy>
- <!-- the default keystore details might need to be edited here -->
-+<!-- Remove all the remaining stuff for this target 
-+     which is only necessary if we want to start jalview
-+     using java web start. It requires us to generate a key 
-+     before building the port - Fernan - 27.Jan.2006 
-       <signjar
-       storepass="alignmentisfun"
-       keypass="alignmentisfun"
-@@ -194,8 +198,9 @@
-       </fileset>
-       </signjar>
-       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
--
-+-->
-       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
-+<!--
-       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
-       codebase="${WebStartLocation}">
-       <information>
-@@ -206,6 +211,7 @@
-         <description kind="short">Jalview</description>
-         <icon href="logo_big.gif"/>
-         <offline_allowed/>
-+-->
- 	<!--
- 	<association mime-type="application-x/ext-file" extensions="fa"/>
-         <association mime-type="application-x/ext-file" extensions="fasta"/>
-@@ -216,6 +222,7 @@
-         <association mime-type="application-x/ext-file" extensions="aln"/>
-         <association mime-type="application-x/ext-file" extensions="pir"/>
- 	-->
-+<!--
-        </information>
-         <resources>
-           <j2se version="1.4+"/>
-@@ -234,6 +241,7 @@
-           <all_permissions/>
-         </security>
-       </jnlp>
-+-->
-     </target>
-     <target name="runenv" depends="init">
-       <path id="run.classpath">
diff --git a/biology/jalview/pkg-descr b/biology/jalview/pkg-descr
index dd89d5cac1a6..4fae9fde95ba 100644
--- a/biology/jalview/pkg-descr
+++ b/biology/jalview/pkg-descr
@@ -22,4 +22,4 @@ o Output alignments as HTML pages, images (PNG) or postscript (EPS).
 If you use Jalview in your work, please quote this publication. Clamp, M., et
 al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7
 
-WWW: http://www.jalview.org
+WWW: https://www.jalview.org
diff --git a/biology/jalview/pkg-plist b/biology/jalview/pkg-plist
deleted file mode 100644
index 763d29468ed4..000000000000
--- a/biology/jalview/pkg-plist
+++ /dev/null
@@ -1,16 +0,0 @@
-bin/jalview
-%%DATADIR%%/activation.jar
-%%DATADIR%%/xercesImpl.jar
-%%DATADIR%%/wsdl4j.jar
-%%DATADIR%%/saaj.jar
-%%DATADIR%%/regex.jar
-%%DATADIR%%/mail.jar
-%%DATADIR%%/log4j-1.2.8.jar
-%%DATADIR%%/jhall.jar
-%%DATADIR%%/jaxrpc.jar
-%%DATADIR%%/jalview.jar
-%%DATADIR%%/commons-logging.jar
-%%DATADIR%%/commons-discovery.jar
-%%DATADIR%%/castor-0.9.6-xml.jar
-%%DATADIR%%/axis.jar
-%%DATADIR%%/xml-apis.jar