git: a4679caacdd4 - main - biology/igv: update 2.16.0 → 2.19.8

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 18 Oct 2026 18:31:31 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a4679caacdd48300992f55fb7eed9be3098d4842

commit a4679caacdd48300992f55fb7eed9be3098d4842
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-10-18 18:31:18 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-10-18 18:31:28 +0000

    biology/igv: update 2.16.0 → 2.19.8
---
 biology/igv/Makefile                 |  38 ++++++----
 biology/igv/distinfo                 |  14 ++--
 biology/igv/files/patch-build.gradle |  25 ++++++
 biology/igv/pkg-plist                | 143 +++++++++++++++++++----------------
 4 files changed, 135 insertions(+), 85 deletions(-)

diff --git a/biology/igv/Makefile b/biology/igv/Makefile
index f5e0af0fad14..0c042a4e3583 100644
--- a/biology/igv/Makefile
+++ b/biology/igv/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	igv
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.16.0
-PORTREVISION=	3
+DISTVERSION=	2.19.8
 CATEGORIES=	biology java
 MASTER_SITES=	http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
 DISTFILES=	tools.png:img
@@ -15,16 +14,15 @@ WWW=		https://software.broadinstitute.org/software/igv/
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/license.txt
 
-BUILD_DEPENDS=	openjfx14>0:java/openjfx14 \
-		gradle:devel/gradle6
-RUN_DEPENDS=	openjfx14>0:java/openjfx14
+BUILD_DEPENDS=	gradle${GRADLE_VER}:devel/gradle${GRADLE_VER}
 
 USES=		gettext-runtime java
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	igvteam
 
-JAVA_VERSION=	11
+JAVA_VERSION=	21
+GRADLE_VER=	8
 
 NO_ARCH=	yes
 
@@ -35,12 +33,13 @@ SUB_FILES=	${PORTNAME}.sh
 DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.png" "${PORTNAME}" \
 		"Biology;Science;" true
 
-# to rebuild the deps archive:
+# How to update (deps archive and pkg-plist are version-specific):
 #   1. set DEV_UPDATE_MODE=yes
-#   2. make makesum build
+#   2. make makesum build  (the *-deps archive is created in ${DISTDIR}/${DIST_SUBDIR})
 #   3. upload the *-deps archive
 #   4. set DEV_UPDATE_MODE=no
 #   5. make clean makesum
+#   6. make stage && make makeplist to regenerate pkg-plist (jar names contain versions)
 
 DEV_UPDATE_MODE=	no
 
@@ -49,11 +48,7 @@ DEPS_CACHE_DIR=	${WRKDIR}
 MAKE_ENV+=	JAVA_HOME=${JAVA_HOME}
 SUB_LIST=	JAVA_HOME=${JAVA_HOME}
 
-.if (${DEV_UPDATE_MODE} == "yes")
-post-build:
-	@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
-	@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
-.else
+.if (${DEV_UPDATE_MODE} != "yes")
 MASTER_SITES+=	LOCAL/yuri/:deps
 DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
 GRADLE_ARGS=	--offline
@@ -63,13 +58,28 @@ post-extract: # need a separate extract step because the cache is in /tmp, and n
 .endif
 
 do-build:
-	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
+	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle${GRADLE_VER} --no-daemon \
 		--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
+		-Porg.gradle.java.installations.paths=${JAVA_HOME} -Porg.gradle.java.installations.auto-download=false \
 		${GRADLE_ARGS} --build-cache --stacktrace createDist
 
+do-test:
+	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle${GRADLE_VER} --no-daemon \
+		--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
+		-Porg.gradle.java.installations.paths=${JAVA_HOME} -Porg.gradle.java.installations.auto-download=false \
+		${GRADLE_ARGS} --no-build-cache test
+
+.if (${DEV_UPDATE_MODE} == "yes")
+post-build: do-test
+	@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
+	@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
+.endif
+
 do-install:
 	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
 	cd ${WRKSRC}/build/IGV-dist/lib && ${COPYTREE_SHARE} ./ ${STAGEDIR}${JAVAJARDIR}/${PORTNAME}
 	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png
 
+# tests as of 2.19.8: 554 tests, 0 failures, 0 errors, 123 skipped
+
 .include <bsd.port.mk>
diff --git a/biology/igv/distinfo b/biology/igv/distinfo
index 55851a42c34e..02a3b16ae2b4 100644
--- a/biology/igv/distinfo
+++ b/biology/igv/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1676844022
-SHA256 (igv-2.16.0/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
-SIZE (igv-2.16.0/tools.png) = 5139
-SHA256 (igv-2.16.0/igv-2.16.0-deps.tar.gz) = 0d853bfafd5a2688f467b76a57bef2c40043f4f62f69f1c40acbe101ec98919f
-SIZE (igv-2.16.0/igv-2.16.0-deps.tar.gz) = 29906082
-SHA256 (igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz) = 1f214e539f8efb726246d6e1f8c3dab9d8fcd8fbe36042f03f052ee73afac2cb
-SIZE (igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz) = 53395541
+TIMESTAMP = 1792344963
+SHA256 (igv-2.19.8/tools.png) = d2721646a4bb9ef248da85639e11eb7bbcf2685396f9b6f8a325b77b127fac4e
+SIZE (igv-2.19.8/tools.png) = 17414
+SHA256 (igv-2.19.8/igv-2.19.8-deps.tar.gz) = cc44c8159e866523634af1eea6a5d5a02acbc2a316fbc61cd1a6090f840607f1
+SIZE (igv-2.19.8/igv-2.19.8-deps.tar.gz) = 49531238
+SHA256 (igv-2.19.8/igvteam-igv-v2.19.8_GH0.tar.gz) = 9845c299996ae8196c71688fe3f950ad5953f80aa952fdeb736009d7c71208be
+SIZE (igv-2.19.8/igvteam-igv-v2.19.8_GH0.tar.gz) = 64953570
diff --git a/biology/igv/files/patch-build.gradle b/biology/igv/files/patch-build.gradle
new file mode 100644
index 000000000000..5e5e5a0481ec
--- /dev/null
+++ b/biology/igv/files/patch-build.gradle
@@ -0,0 +1,25 @@
+-- Make unit tests runnable: pass the real working directory to the test JVM (the inherited user.dir
+-- breaks relative test data paths) and skip tests that need network access.
+
+--- build.gradle.orig	2026-10-18 08:58:23 UTC
++++ build.gradle
+@@ -193,6 +193,7 @@ tasks.withType(Test).configureEach {
+ tasks.withType(Test).configureEach {
+     systemProperties.clear()
+     systemProperties.putAll( System.getProperties() )
++    systemProperties['user.dir'] = projectDir.absolutePath
+     systemProperties['java.awt.headless'] = 'true'
+     systemProperties['make.fail'] = 'false'
+     systemProperties['include.longrunning'] = 'false'
+@@ -201,6 +202,11 @@ tasks.withType(Test).configureEach {
+     maxHeapSize = '2g'
+     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
+     useJUnitPlatform()
++    filter {
++        // these tests need network access
++        excludeTestsMatching '*Htsget*'
++        excludeTestsMatching '*FileFormatUtilsTest.testDetermineFormat'
++    }
+ }
+ 
+ tasks.register('createDist', Copy) {
diff --git a/biology/igv/pkg-plist b/biology/igv/pkg-plist
index c198824feb0e..d2e9f5847337 100644
--- a/biology/igv/pkg-plist
+++ b/biology/igv/pkg-plist
@@ -1,31 +1,41 @@
 bin/igv
-%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar
-%%JAVAJARDIR%%/igv/annotations-2.16.7.jar
-%%JAVAJARDIR%%/igv/apache-client-2.16.7.jar
-%%JAVAJARDIR%%/igv/arns-2.16.7.jar
-%%JAVAJARDIR%%/igv/auth-2.16.7.jar
-%%JAVAJARDIR%%/igv/aws-core-2.16.7.jar
-%%JAVAJARDIR%%/igv/aws-json-protocol-2.16.7.jar
-%%JAVAJARDIR%%/igv/aws-query-protocol-2.16.7.jar
-%%JAVAJARDIR%%/igv/aws-xml-protocol-2.16.7.jar
-%%JAVAJARDIR%%/igv/batik-awt-util-1.11.jar
-%%JAVAJARDIR%%/igv/batik-codec-1.11.jar
-%%JAVAJARDIR%%/igv/batik-constants-1.11.jar
-%%JAVAJARDIR%%/igv/batik-dom-1.11.jar
-%%JAVAJARDIR%%/igv/batik-ext-1.11.jar
-%%JAVAJARDIR%%/igv/batik-i18n-1.11.jar
-%%JAVAJARDIR%%/igv/batik-svggen-1.11.jar
-%%JAVAJARDIR%%/igv/batik-transcoder-1.11.jar
-%%JAVAJARDIR%%/igv/batik-util-1.11.jar
-%%JAVAJARDIR%%/igv/batik-xml-1.11.jar
-%%JAVAJARDIR%%/igv/cognitoidentity-2.16.7.jar
-%%JAVAJARDIR%%/igv/commons-codec-1.11.jar
-%%JAVAJARDIR%%/igv/commons-compress-1.19.jar
-%%JAVAJARDIR%%/igv/commons-io-2.6.jar
-%%JAVAJARDIR%%/igv/commons-jexl-2.1.1.jar
-%%JAVAJARDIR%%/igv/commons-lang3-3.9.jar
-%%JAVAJARDIR%%/igv/commons-logging-1.2.jar
-%%JAVAJARDIR%%/igv/commons-math3-3.6.1.jar
+%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110-module.jar
+%%JAVAJARDIR%%/igv/annotations-2.30.17.jar
+%%JAVAJARDIR%%/igv/apache-client-2.30.17.jar
+%%JAVAJARDIR%%/igv/arns-2.30.17.jar
+%%JAVAJARDIR%%/igv/asm-7.3.1.jar
+%%JAVAJARDIR%%/igv/asm-analysis-7.3.1.jar
+%%JAVAJARDIR%%/igv/asm-commons-7.3.1.jar
+%%JAVAJARDIR%%/igv/asm-tree-7.3.1.jar
+%%JAVAJARDIR%%/igv/asm-util-7.3.1.jar
+%%JAVAJARDIR%%/igv/auth-2.30.17.jar
+%%JAVAJARDIR%%/igv/aws-core-2.30.17.jar
+%%JAVAJARDIR%%/igv/aws-json-protocol-2.30.17.jar
+%%JAVAJARDIR%%/igv/aws-query-protocol-2.30.17.jar
+%%JAVAJARDIR%%/igv/aws-xml-protocol-2.30.17.jar
+%%JAVAJARDIR%%/igv/batik-awt-util-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-codec-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-constants-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-dom-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-ext-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-i18n-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-shared-resources-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-svggen-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-transcoder-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-util-1.17-module.jar
+%%JAVAJARDIR%%/igv/batik-xml-1.17-module.jar
+%%JAVAJARDIR%%/igv/checksums-2.30.17.jar
+%%JAVAJARDIR%%/igv/checksums-spi-2.30.17.jar
+%%JAVAJARDIR%%/igv/cognitoidentity-2.30.17.jar
+%%JAVAJARDIR%%/igv/commons-codec-1.17.1.jar
+%%JAVAJARDIR%%/igv/commons-compress-1.26.0.jar
+%%JAVAJARDIR%%/igv/commons-io-2.15.1.jar
+%%JAVAJARDIR%%/igv/commons-jexl-2.1.1-module.jar
+%%JAVAJARDIR%%/igv/commons-lang3-3.14.0.jar
+%%JAVAJARDIR%%/igv/commons-logging-1.3.0.jar
+%%JAVAJARDIR%%/igv/commons-math3-3.6.1-module.jar
+%%JAVAJARDIR%%/igv/crt-core-2.30.17.jar
+%%JAVAJARDIR%%/igv/endpoints-spi-2.30.17.jar
 %%JAVAJARDIR%%/igv/eventstream-1.0.1.jar
 %%JAVAJARDIR%%/igv/genomes/129S1_SvImJ.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/1kg_ref.chrom.sizes
@@ -233,43 +243,48 @@ bin/igv
 %%JAVAJARDIR%%/igv/genomes/xenTro2.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/xenTro9.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/zebrafish.chrom.sizes
-%%JAVAJARDIR%%/igv/gson-2.8.5.jar
-%%JAVAJARDIR%%/igv/guava-27.0.1-jre.jar
-%%JAVAJARDIR%%/igv/htsjdk-3.0.0.jar
-%%JAVAJARDIR%%/igv/http-client-spi-2.16.7.jar
+%%JAVAJARDIR%%/igv/gson-2.8.9.jar
+%%JAVAJARDIR%%/igv/guava-32.1.3-jre.jar
+%%JAVAJARDIR%%/igv/htsjdk-4.3.0-module.jar
+%%JAVAJARDIR%%/igv/http-auth-2.30.17.jar
+%%JAVAJARDIR%%/igv/http-auth-aws-2.30.17.jar
+%%JAVAJARDIR%%/igv/http-auth-aws-eventstream-2.30.17.jar
+%%JAVAJARDIR%%/igv/http-auth-spi-2.30.17.jar
+%%JAVAJARDIR%%/igv/http-client-spi-2.30.17.jar
 %%JAVAJARDIR%%/igv/httpclient-4.5.13.jar
-%%JAVAJARDIR%%/igv/httpcore-4.4.13.jar
+%%JAVAJARDIR%%/igv/httpcore-4.4.16.jar
+%%JAVAJARDIR%%/igv/identity-spi-2.30.17.jar
 %%JAVAJARDIR%%/igv/igv.jar
-%%JAVAJARDIR%%/igv/j2objc-annotations-1.1.jar
-%%JAVAJARDIR%%/igv/jackson-annotations-2.12.1.jar
-%%JAVAJARDIR%%/igv/jackson-core-2.12.1.jar
-%%JAVAJARDIR%%/igv/jackson-databind-2.12.1.jar
-%%JAVAJARDIR%%/igv/jide-common-3.7.3.jar
-%%JAVAJARDIR%%/igv/metrics-spi-2.16.7.jar
-%%JAVAJARDIR%%/igv/mjson-1.4.1.jar
-%%JAVAJARDIR%%/igv/netty-buffer-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-codec-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-codec-http-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-common-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-handler-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-nio-client-2.16.7.jar
-%%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.4.jar
-%%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.4.jar
-%%JAVAJARDIR%%/igv/netty-resolver-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-transport-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.59.Final-linux-x86_64.jar
-%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.59.Final.jar
-%%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar
-%%JAVAJARDIR%%/igv/profiles-2.16.7.jar
-%%JAVAJARDIR%%/igv/protocol-core-2.16.7.jar
-%%JAVAJARDIR%%/igv/reactive-streams-1.0.3.jar
-%%JAVAJARDIR%%/igv/regions-2.16.7.jar
-%%JAVAJARDIR%%/igv/s3-2.16.7.jar
-%%JAVAJARDIR%%/igv/sdk-core-2.16.7.jar
-%%JAVAJARDIR%%/igv/slf4j-api-1.7.28.jar
-%%JAVAJARDIR%%/igv/snappy-java-1.1.8.4.jar
-%%JAVAJARDIR%%/igv/sts-2.16.7.jar
-%%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar
-%%JAVAJARDIR%%/igv/utils-2.16.7.jar
-%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar
+%%JAVAJARDIR%%/igv/jide-oss-3.7.12-module.jar
+%%JAVAJARDIR%%/igv/json-20231013.jar
+%%JAVAJARDIR%%/igv/json-utils-2.30.17.jar
+%%JAVAJARDIR%%/igv/metrics-spi-2.30.17.jar
+%%JAVAJARDIR%%/igv/nashorn-core-15.4.jar
+%%JAVAJARDIR%%/igv/netty-buffer-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-codec-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-codec-http-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-common-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-handler-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-nio-client-2.30.17.jar
+%%JAVAJARDIR%%/igv/netty-resolver-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-transport-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-transport-classes-epoll-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.118.Final.jar
+%%JAVAJARDIR%%/igv/ngs-java-2.9.0-module.jar
+%%JAVAJARDIR%%/igv/profiles-2.30.17.jar
+%%JAVAJARDIR%%/igv/protocol-core-2.30.17.jar
+%%JAVAJARDIR%%/igv/reactive-streams-1.0.4.jar
+%%JAVAJARDIR%%/igv/regions-2.30.17.jar
+%%JAVAJARDIR%%/igv/retries-2.30.17.jar
+%%JAVAJARDIR%%/igv/retries-spi-2.30.17.jar
+%%JAVAJARDIR%%/igv/s3-2.30.17.jar
+%%JAVAJARDIR%%/igv/sdk-core-2.30.17.jar
+%%JAVAJARDIR%%/igv/slf4j-api-1.7.36.jar
+%%JAVAJARDIR%%/igv/sso-2.30.17.jar
+%%JAVAJARDIR%%/igv/sts-2.30.17.jar
+%%JAVAJARDIR%%/igv/swing-layout-1.0.3-module.jar
+%%JAVAJARDIR%%/igv/third-party-jackson-core-2.30.17.jar
+%%JAVAJARDIR%%/igv/utils-2.30.17.jar
+%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.9-module.jar
+%%JAVAJARDIR%%/igv/xz-1.9.jar
 share/pixmaps/igv.png