biology/igv: Update 2.8.13 -> 2.9.4

3 files changed, 44 insertions, 42 deletions

diff --git a/biology/igv/Makefile b/biology/igv/Makefile
index 694c647cfa2b..188c13230261 100644
--- a/biology/igv/Makefile
+++ b/biology/igv/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	igv
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.8.13
+DISTVERSION=	2.9.4
 CATEGORIES=	biology java
 MASTER_SITES=	http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
 DISTFILES=	tools.png:img
@@ -33,7 +33,7 @@ MAKE_ENV+=	GRADLE_USER_HOME=${WRKDIR}
 
 SUB_FILES=	${PORTNAME}.sh
 
-DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \
+DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.png" "${PORTNAME}" \
 		"Biology;Science;" true
 
 # to rebuild the deps archive:
@@ -52,7 +52,7 @@ SUB_LIST=	JAVA_HOME=${JAVA_HOME}
 
 .if (${DEV_UPDATE_MODE} == "yes")
 post-build:
-	@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
+	@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
 MASTER_SITES+=	LOCAL/yuri/:deps
diff --git a/biology/igv/distinfo b/biology/igv/distinfo
index ac0c19b035c6..6f96ea31b8f8 100644
--- a/biology/igv/distinfo
+++ b/biology/igv/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1606697368
-SHA256 (igv-2.8.13/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
-SIZE (igv-2.8.13/tools.png) = 5139
-SHA256 (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 0bea74c4e1934fba8273c91ed9a6c2e88540b96823a8b8d4cf5c3d82617f330a
-SIZE (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 54089812
-SHA256 (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 891d3874ab2bc75d54c8f3ae8bc1df6b0b4b8b3f371d8699b17c69cbace77e7c
-SIZE (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 122357224
+TIMESTAMP = 1616904994
+SHA256 (igv-2.9.4/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
+SIZE (igv-2.9.4/tools.png) = 5139
+SHA256 (igv-2.9.4/igv-2.9.4-deps.tar.gz) = 034056e5d8f5ddbd4575fd337d81cfe7fdea172e1ae8a043103dae2aa74be070
+SIZE (igv-2.9.4/igv-2.9.4-deps.tar.gz) = 54460338
+SHA256 (igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz) = 1c40f286fd0baf62a8f1b813d535200f8829fc489ba40944b2c8483b66c3b4a1
+SIZE (igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz) = 121959982
diff --git a/biology/igv/pkg-plist b/biology/igv/pkg-plist
index 8eb716eb3d6e..28e6071b98ea 100644
--- a/biology/igv/pkg-plist
+++ b/biology/igv/pkg-plist
@@ -1,12 +1,13 @@
 bin/igv
 %%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar
-%%JAVAJARDIR%%/igv/apache-client-2.15.9.jar
-%%JAVAJARDIR%%/igv/arns-2.15.9.jar
-%%JAVAJARDIR%%/igv/auth-2.15.9.jar
-%%JAVAJARDIR%%/igv/aws-core-2.15.9.jar
-%%JAVAJARDIR%%/igv/aws-json-protocol-2.15.9.jar
-%%JAVAJARDIR%%/igv/aws-query-protocol-2.15.9.jar
-%%JAVAJARDIR%%/igv/aws-xml-protocol-2.15.9.jar
+%%JAVAJARDIR%%/igv/annotations-2.15.67.jar
+%%JAVAJARDIR%%/igv/apache-client-2.15.67.jar
+%%JAVAJARDIR%%/igv/arns-2.15.67.jar
+%%JAVAJARDIR%%/igv/auth-2.15.67.jar
+%%JAVAJARDIR%%/igv/aws-core-2.15.67.jar
+%%JAVAJARDIR%%/igv/aws-json-protocol-2.15.67.jar
+%%JAVAJARDIR%%/igv/aws-query-protocol-2.15.67.jar
+%%JAVAJARDIR%%/igv/aws-xml-protocol-2.15.67.jar
 %%JAVAJARDIR%%/igv/batik-awt-util-1.11.jar
 %%JAVAJARDIR%%/igv/batik-codec-1.11.jar
 %%JAVAJARDIR%%/igv/batik-constants-1.11.jar
@@ -17,7 +18,7 @@ bin/igv
 %%JAVAJARDIR%%/igv/batik-transcoder-1.11.jar
 %%JAVAJARDIR%%/igv/batik-util-1.11.jar
 %%JAVAJARDIR%%/igv/batik-xml-1.11.jar
-%%JAVAJARDIR%%/igv/cognitoidentity-2.15.9.jar
+%%JAVAJARDIR%%/igv/cognitoidentity-2.15.67.jar
 %%JAVAJARDIR%%/igv/commons-codec-1.11.jar
 %%JAVAJARDIR%%/igv/commons-collections-20040616.jar
 %%JAVAJARDIR%%/igv/commons-compress-1.19.jar
@@ -116,6 +117,7 @@ bin/igv
 %%JAVAJARDIR%%/igv/genomes/ca21.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/canFam2.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/canFam3.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/canFam4.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/candida.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/cavPor3.chrom.sizes
 %%JAVAJARDIR%%/igv/genomes/ce10.chrom.sizes
@@ -216,46 +218,46 @@ bin/igv
 %%JAVAJARDIR%%/igv/gson-2.8.5.jar
 %%JAVAJARDIR%%/igv/guava-27.0.1-jre.jar
 %%JAVAJARDIR%%/igv/htsjdk-2.23.0.jar
-%%JAVAJARDIR%%/igv/http-client-spi-2.15.9.jar
-%%JAVAJARDIR%%/igv/httpclient-4.5.9.jar
-%%JAVAJARDIR%%/igv/httpcore-4.4.11.jar
+%%JAVAJARDIR%%/igv/http-client-spi-2.15.67.jar
+%%JAVAJARDIR%%/igv/httpclient-4.5.13.jar
+%%JAVAJARDIR%%/igv/httpcore-4.4.13.jar
 %%JAVAJARDIR%%/igv/icb-utils-2.0.2.jar
 %%JAVAJARDIR%%/igv/igv.jar
 %%JAVAJARDIR%%/igv/j2objc-annotations-1.1.jar
-%%JAVAJARDIR%%/igv/jackson-annotations-2.10.4.jar
-%%JAVAJARDIR%%/igv/jackson-core-2.10.4.jar
-%%JAVAJARDIR%%/igv/jackson-databind-2.10.4.jar
+%%JAVAJARDIR%%/igv/jackson-annotations-2.10.5.jar
+%%JAVAJARDIR%%/igv/jackson-core-2.10.5.jar
+%%JAVAJARDIR%%/igv/jackson-databind-2.10.5.1.jar
 %%JAVAJARDIR%%/igv/jide-common-3.7.3.jar
 %%JAVAJARDIR%%/igv/jsap-3.0.0.jar
 %%JAVAJARDIR%%/igv/log4j-1.2-api-2.11.0.jar
 %%JAVAJARDIR%%/igv/log4j-api-2.11.0.jar
 %%JAVAJARDIR%%/igv/log4j-core-2.11.0.jar
-%%JAVAJARDIR%%/igv/metrics-spi-2.15.9.jar
-%%JAVAJARDIR%%/igv/netty-buffer-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-codec-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-codec-http-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-common-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-handler-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-nio-client-2.15.9.jar
+%%JAVAJARDIR%%/igv/metrics-spi-2.15.67.jar
+%%JAVAJARDIR%%/igv/netty-buffer-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-codec-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-codec-http-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-common-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-handler-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-nio-client-2.15.67.jar
 %%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.4.jar
 %%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.4.jar
-%%JAVAJARDIR%%/igv/netty-resolver-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-transport-4.1.46.Final.jar
-%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.46.Final-linux-x86_64.jar
-%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.46.Final.jar
+%%JAVAJARDIR%%/igv/netty-resolver-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-transport-4.1.53.Final.jar
+%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.53.Final-linux-x86_64.jar
+%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.53.Final.jar
 %%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar
-%%JAVAJARDIR%%/igv/profiles-2.15.9.jar
+%%JAVAJARDIR%%/igv/profiles-2.15.67.jar
 %%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar
-%%JAVAJARDIR%%/igv/protocol-core-2.15.9.jar
+%%JAVAJARDIR%%/igv/protocol-core-2.15.67.jar
 %%JAVAJARDIR%%/igv/reactive-streams-1.0.3.jar
-%%JAVAJARDIR%%/igv/regions-2.15.9.jar
-%%JAVAJARDIR%%/igv/s3-2.15.9.jar
-%%JAVAJARDIR%%/igv/sdk-core-2.15.9.jar
+%%JAVAJARDIR%%/igv/regions-2.15.67.jar
+%%JAVAJARDIR%%/igv/s3-2.15.67.jar
+%%JAVAJARDIR%%/igv/sdk-core-2.15.67.jar
 %%JAVAJARDIR%%/igv/slf4j-api-1.7.28.jar
 %%JAVAJARDIR%%/igv/slf4j-simple-1.7.26.jar
 %%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar
-%%JAVAJARDIR%%/igv/sts-2.15.9.jar
+%%JAVAJARDIR%%/igv/sts-2.15.67.jar
 %%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar
-%%JAVAJARDIR%%/igv/utils-2.15.9.jar
+%%JAVAJARDIR%%/igv/utils-2.15.67.jar
 %%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar
 share/pixmaps/igv.png