igv: Update to 2.9.2, add local pkgsrc JAVA_HOME, clean up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: igv: Update to 2.9.2, add local pkgsrc JAVA_HOME, clean up
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Tue, 23 Feb 2021 15:35:14 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Feb 23 09:35:14 2021 -0600
Changeset:	4796874833bbf837e13cd616765b50c520cf974c

Modified Files:
	igv/Makefile
	igv/PLIST
	igv/distinfo
	igv/files/igv.sh.in

Log Message:
igv: Update to 2.9.2, add local pkgsrc JAVA_HOME, clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4796874833bbf837e13cd616765b50c520cf974c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 igv/Makefile        | 16 +++++--------
 igv/PLIST           | 66 ++++++++++++++++++++++++++---------------------------
 igv/distinfo        |  8 +++----
 igv/files/igv.sh.in |  5 +++-
 4 files changed, 47 insertions(+), 48 deletions(-)

diffs:
diff --git a/igv/Makefile b/igv/Makefile
index d1a537bc7d..82918ea400 100644
--- a/igv/Makefile
+++ b/igv/Makefile
@@ -1,14 +1,9 @@
 # $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Mon Feb 22 13:21:20 CST 2021               #
-###########################################################
 
 DISTNAME=	IGV_${PKGVERSION_NOREV}
-PKGNAME=	igv-2.8.13
+PKGNAME=	igv-2.9.2
 CATEGORIES=	biology
-MASTER_SITES=	https://data.broadinstitute.org/igv/projects/downloads/2.8/
+MASTER_SITES=	https://data.broadinstitute.org/igv/projects/downloads/2.9/
 EXTRACT_SUFX=	.zip
 
 MAINTAINER=	bacon%NetBSD.org@localhost
@@ -23,13 +18,14 @@ NO_BUILD=	yes
 
 SUBST_CLASSES+=		java
 SUBST_STAGE.java=	pre-configure
-SUBST_SED.java+=	-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
+SUBST_SED.java=		-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
+SUBST_SED.java+=	-e 's|%%PREFIX%%|${PREFIX}|g'
 SUBST_FILES.java=	igv
 
 JAVAJARDIR=		${PREFIX}/share/java/classes
-INSTALLATION_DIRS=	bin share/pixmaps ${JAVAJARDIR}/igv
+INSTALLATION_DIRS=	bin ${JAVAJARDIR}/igv
 
-post-extract:
+pre-patch:
 	${CP} ${FILESDIR}/igv.sh.in ${WRKSRC}/igv
 
 do-install:
diff --git a/igv/PLIST b/igv/PLIST
index ef893d0af4..1135245748 100644
--- a/igv/PLIST
+++ b/igv/PLIST
@@ -1,14 +1,14 @@
 @comment $NetBSD$
 bin/igv
 share/java/classes/igv/AbsoluteLayout-RELEASE110.jar
-share/java/classes/igv/annotations-2.15.9.jar
-share/java/classes/igv/apache-client-2.15.9.jar
-share/java/classes/igv/arns-2.15.9.jar
-share/java/classes/igv/auth-2.15.9.jar
-share/java/classes/igv/aws-core-2.15.9.jar
-share/java/classes/igv/aws-json-protocol-2.15.9.jar
-share/java/classes/igv/aws-query-protocol-2.15.9.jar
-share/java/classes/igv/aws-xml-protocol-2.15.9.jar
+share/java/classes/igv/annotations-2.15.67.jar
+share/java/classes/igv/apache-client-2.15.67.jar
+share/java/classes/igv/arns-2.15.67.jar
+share/java/classes/igv/auth-2.15.67.jar
+share/java/classes/igv/aws-core-2.15.67.jar
+share/java/classes/igv/aws-json-protocol-2.15.67.jar
+share/java/classes/igv/aws-query-protocol-2.15.67.jar
+share/java/classes/igv/aws-xml-protocol-2.15.67.jar
 share/java/classes/igv/batik-awt-util-1.11.jar
 share/java/classes/igv/batik-codec-1.11.jar
 share/java/classes/igv/batik-constants-1.11.jar
@@ -19,7 +19,7 @@ share/java/classes/igv/batik-svggen-1.11.jar
 share/java/classes/igv/batik-transcoder-1.11.jar
 share/java/classes/igv/batik-util-1.11.jar
 share/java/classes/igv/batik-xml-1.11.jar
-share/java/classes/igv/cognitoidentity-2.15.9.jar
+share/java/classes/igv/cognitoidentity-2.15.67.jar
 share/java/classes/igv/commons-codec-1.11.jar
 share/java/classes/igv/commons-collections-20040616.jar
 share/java/classes/igv/commons-compress-1.19.jar
@@ -219,46 +219,46 @@ share/java/classes/igv/goby-io-3.3.1.jar
 share/java/classes/igv/gson-2.8.5.jar
 share/java/classes/igv/guava-27.0.1-jre.jar
 share/java/classes/igv/htsjdk-2.23.0.jar
-share/java/classes/igv/http-client-spi-2.15.9.jar
-share/java/classes/igv/httpclient-4.5.9.jar
-share/java/classes/igv/httpcore-4.4.11.jar
+share/java/classes/igv/http-client-spi-2.15.67.jar
+share/java/classes/igv/httpclient-4.5.13.jar
+share/java/classes/igv/httpcore-4.4.13.jar
 share/java/classes/igv/icb-utils-2.0.2.jar
 share/java/classes/igv/igv.args
 share/java/classes/igv/igv.jar
 share/java/classes/igv/j2objc-annotations-1.1.jar
-share/java/classes/igv/jackson-annotations-2.10.4.jar
-share/java/classes/igv/jackson-core-2.10.4.jar
-share/java/classes/igv/jackson-databind-2.10.4.jar
+share/java/classes/igv/jackson-annotations-2.10.5.jar
+share/java/classes/igv/jackson-core-2.10.5.jar
+share/java/classes/igv/jackson-databind-2.10.5.1.jar
 share/java/classes/igv/jide-common-3.7.3.jar
 share/java/classes/igv/jsap-3.0.0.jar
 share/java/classes/igv/log4j-1.2-api-2.11.0.jar
 share/java/classes/igv/log4j-api-2.11.0.jar
 share/java/classes/igv/log4j-core-2.11.0.jar
-share/java/classes/igv/metrics-spi-2.15.9.jar
-share/java/classes/igv/netty-buffer-4.1.46.Final.jar
-share/java/classes/igv/netty-codec-4.1.46.Final.jar
-share/java/classes/igv/netty-codec-http-4.1.46.Final.jar
-share/java/classes/igv/netty-common-4.1.46.Final.jar
-share/java/classes/igv/netty-handler-4.1.46.Final.jar
-share/java/classes/igv/netty-nio-client-2.15.9.jar
+share/java/classes/igv/metrics-spi-2.15.67.jar
+share/java/classes/igv/netty-buffer-4.1.53.Final.jar
+share/java/classes/igv/netty-codec-4.1.53.Final.jar
+share/java/classes/igv/netty-codec-http-4.1.53.Final.jar
+share/java/classes/igv/netty-common-4.1.53.Final.jar
+share/java/classes/igv/netty-handler-4.1.53.Final.jar
+share/java/classes/igv/netty-nio-client-2.15.67.jar
 share/java/classes/igv/netty-reactive-streams-2.0.4.jar
 share/java/classes/igv/netty-reactive-streams-http-2.0.4.jar
-share/java/classes/igv/netty-resolver-4.1.46.Final.jar
-share/java/classes/igv/netty-transport-4.1.46.Final.jar
-share/java/classes/igv/netty-transport-native-epoll-4.1.46.Final-linux-x86_64.jar
-share/java/classes/igv/netty-transport-native-unix-common-4.1.46.Final.jar
+share/java/classes/igv/netty-resolver-4.1.53.Final.jar
+share/java/classes/igv/netty-transport-4.1.53.Final.jar
+share/java/classes/igv/netty-transport-native-epoll-4.1.53.Final-linux-x86_64.jar
+share/java/classes/igv/netty-transport-native-unix-common-4.1.53.Final.jar
 share/java/classes/igv/ngs-java-2.9.0.jar
-share/java/classes/igv/profiles-2.15.9.jar
+share/java/classes/igv/profiles-2.15.67.jar
 share/java/classes/igv/protobuf-java-3.7.0-rc1.jar
-share/java/classes/igv/protocol-core-2.15.9.jar
+share/java/classes/igv/protocol-core-2.15.67.jar
 share/java/classes/igv/reactive-streams-1.0.3.jar
-share/java/classes/igv/regions-2.15.9.jar
-share/java/classes/igv/s3-2.15.9.jar
-share/java/classes/igv/sdk-core-2.15.9.jar
+share/java/classes/igv/regions-2.15.67.jar
+share/java/classes/igv/s3-2.15.67.jar
+share/java/classes/igv/sdk-core-2.15.67.jar
 share/java/classes/igv/slf4j-api-1.7.28.jar
 share/java/classes/igv/slf4j-simple-1.7.26.jar
 share/java/classes/igv/snappy-java-1.1.7.3.jar
-share/java/classes/igv/sts-2.15.9.jar
+share/java/classes/igv/sts-2.15.67.jar
 share/java/classes/igv/swing-layout-1.0.3.jar
-share/java/classes/igv/utils-2.15.9.jar
+share/java/classes/igv/utils-2.15.67.jar
 share/java/classes/igv/xmlgraphics-commons-2.3.jar
diff --git a/igv/distinfo b/igv/distinfo
index 298464bc40..f51290cde0 100644
--- a/igv/distinfo
+++ b/igv/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (IGV_2.8.13.zip) = af6c68521604b4e51940abbadf39107b2e33c9f2
-RMD160 (IGV_2.8.13.zip) = 80c9f1e6454d248847ea504c1cbba8716e04fc44
-SHA512 (IGV_2.8.13.zip) = 0b8551871560cd0bb36f2783e12c4031e38330f57f80e4cbf6ac0d72227fc297c012b23e579c171c49b092e7b8e07cbc08fb5e1845abb7e57d3cb079b4f54151
-Size (IGV_2.8.13.zip) = 55544498 bytes
+SHA1 (IGV_2.9.2.zip) = 873b273f25b757f4f808fff690b0d4d0f55dea39
+RMD160 (IGV_2.9.2.zip) = 1f44e603d55cee22a64eedbb874b75f6efa77835
+SHA512 (IGV_2.9.2.zip) = 6c8156401b0ba760f59b50a8004dcd025d0f6ac6a86776a6928af857c6d4309c914d2552fdde0dd89eddf443d7e18ab7b0fa9db15737701815cf3190a78b4c30
+Size (IGV_2.9.2.zip) = 55890979 bytes
diff --git a/igv/files/igv.sh.in b/igv/files/igv.sh.in
index 281f1131df..0b87c996d4 100755
--- a/igv/files/igv.sh.in
+++ b/igv/files/igv.sh.in
@@ -3,8 +3,11 @@
 if [ -e /usr/libexec/java_home ]; then
     # MacOS openjdk
     export JAVA_HOME=$(/usr/libexec/java_home)
+elif [ -e %%PREFIX%%/java/openjdk11/bin/java ]; then
+    # Custom pkgsrc
+    export JAVA_HOME=%%PREFIX%%/java/openjdk11
 elif [ -e /usr/pkg/java/openjdk11/bin/java ]; then
-    # Pkgsrc
+    # Try NetBSD default pkgsrc if not installed in the custom tree
     export JAVA_HOME=/usr/pkg/java/openjdk11
 fi
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