From 1caf88f57ec7a9dd50531c0bd096310b4164e248 Mon Sep 17 00:00:00 2001
From: Yuri Victorovich <yuri@FreeBSD.org>
Date: Sun, 4 Nov 2018 22:55:24 +0000
Subject: [PATCH] biology/igv: Update 2.4.10 -> 2.4.15

Port changes:
* Change to gradle, corresponding updates in build, install, environment, etc.

Reported by:	portscout
---
 biology/igv/Makefile              | 25 ++++++++++++++++---------
 biology/igv/distinfo              | 10 +++++-----
 biology/igv/files/patch-build.xml | 10 ----------
 3 files changed, 21 insertions(+), 24 deletions(-)
 delete mode 100644 biology/igv/files/patch-build.xml

diff --git a/biology/igv/Makefile b/biology/igv/Makefile
index 367c84948ab8..8dba653e3cfe 100644
--- a/biology/igv/Makefile
+++ b/biology/igv/Makefile
@@ -2,9 +2,9 @@
 
 PORTNAME=	igv
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.10
+DISTVERSION=	2.4.15
 CATEGORIES=	biology java
-MASTER_SITES=	http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
+MASTER_SITES=	http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
 DISTFILES=	tools.png:img
 DIST_SUBDIR=	${PORTNAME}-${DISTVERSION}
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
@@ -15,32 +15,39 @@ COMMENT=	Visualization tool for genomic datasets
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/license.txt
 
-BUILD_DEPENDS=	openjfx8-devel>0:java/openjfx8-devel
+BUILD_DEPENDS=	openjfx8-devel>0:java/openjfx8-devel \
+		gradle:devel/gradle
 RUN_DEPENDS=	openjfx8-devel>0:java/openjfx8-devel
 
 USES=		gettext-runtime
 USE_GITHUB=	yes
 GH_ACCOUNT=	igvteam
 USE_JAVA=	yes
-USE_ANT=	yes
 NO_ARCH=	yes
 
+MAKE_ENV+=	GRADLE_USER_HOME=${WRKDIR}
+
 SUB_FILES=	${PORTNAME}.sh
 
 DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \
 		"Biology;Science;" true
 
 PLIST_FILES=	bin/${PORTNAME} \
-		${JAVAJARDIR}/batik-codec__V1.7.jar \
-		${JAVAJARDIR}/goby-io-igv__V1.0.jar \
+		${JAVAJARDIR}/batik-codec-1.10.jar \
+		${JAVAJARDIR}/goby-io-igv-1.1.jar \
+		${JAVAJARDIR}/log4j-core-2.11.0.jar \
 		${JAVAJARDIR}/${PORTNAME}.jar \
 		share/pixmaps/igv.png
 
+do-build:
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle createDist
+
 do-install:
 	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
-	${INSTALL_DATA} ${WRKSRC}/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR}
-	${INSTALL_DATA} ${WRKSRC}/batik-codec__V1.7.jar ${STAGEDIR}${JAVAJARDIR}
-	${INSTALL_DATA} ${WRKSRC}/goby-io-igv__V1.0.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/batik-codec-1.10.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/goby-io-igv-1.1.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/log4j-core-2.11.0.jar ${STAGEDIR}${JAVAJARDIR}
 	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png
 
 .include <bsd.port.mk>
diff --git a/biology/igv/distinfo b/biology/igv/distinfo
index 76f41bfff53b..3c847ab54673 100644
--- a/biology/igv/distinfo
+++ b/biology/igv/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1529969906
-SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
-SIZE (igv-2.4.10/tools.png) = 5139
-SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73
-SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902
+TIMESTAMP = 1541357814
+SHA256 (igv-2.4.15/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
+SIZE (igv-2.4.15/tools.png) = 5139
+SHA256 (igv-2.4.15/igvteam-igv-v2.4.15_GH0.tar.gz) = 8cd1da4a90b3607fd1d2840877497afa8a11b2bdbb69d1ead02ca401153ce6b0
+SIZE (igv-2.4.15/igvteam-igv-v2.4.15_GH0.tar.gz) = 141294377
diff --git a/biology/igv/files/patch-build.xml b/biology/igv/files/patch-build.xml
deleted file mode 100644
index b65970df3df9..000000000000
--- a/biology/igv/files/patch-build.xml
+++ /dev/null
@@ -1,10 +0,0 @@
---- build.xml.orig	2018-06-25 21:00:29 UTC
-+++ build.xml
-@@ -177,6 +177,7 @@
-         <sequential>
-             <jar destfile="${jar.path}" basedir="${tmp.dir}" compress="true" duplicate="preserve">
-                 <fileset refid="@{includedFileset}"/>
-+                <zipgroupfileset dir="${lib.dir}" includes="**/*.jar" />
-                 <manifest>
- 
-                     <attribute name="Permissions" value="all-permissions"/>