git: b021237b2dda - main - biology/igv: Update 2.9.4 → 2.16.0
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Date: Mon, 20 Feb 2023 07:20:52 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=b021237b2dda0a5c47aa770ea37bf8db96e4951b
commit b021237b2dda0a5c47aa770ea37bf8db96e4951b
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-02-20 07:19:23 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-02-20 07:20:49 +0000
biology/igv: Update 2.9.4 → 2.16.0
PR: 269690
Reported by: jwb@
---
biology/igv/Makefile | 2 +-
biology/igv/distinfo | 14 +++----
biology/igv/pkg-plist | 104 ++++++++++++++++++++++++++++----------------------
3 files changed, 66 insertions(+), 54 deletions(-)
diff --git a/biology/igv/Makefile b/biology/igv/Makefile
index 4018c31c67b5..c355a14924d0 100644
--- a/biology/igv/Makefile
+++ b/biology/igv/Makefile
@@ -1,6 +1,6 @@
PORTNAME= igv
DISTVERSIONPREFIX= v
-DISTVERSION= 2.9.4
+DISTVERSION= 2.16.0
CATEGORIES= biology java
MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
DISTFILES= tools.png:img
diff --git a/biology/igv/distinfo b/biology/igv/distinfo
index 6f96ea31b8f8..55851a42c34e 100644
--- a/biology/igv/distinfo
+++ b/biology/igv/distinfo
@@ -1,7 +1,7 @@
-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
+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
diff --git a/biology/igv/pkg-plist b/biology/igv/pkg-plist
index 28e6071b98ea..c198824feb0e 100644
--- a/biology/igv/pkg-plist
+++ b/biology/igv/pkg-plist
@@ -1,13 +1,13 @@
bin/igv
%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.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/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
@@ -18,26 +18,27 @@ 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-2.15.67.jar
+%%JAVAJARDIR%%/igv/cognitoidentity-2.16.7.jar
%%JAVAJARDIR%%/igv/commons-codec-1.11.jar
-%%JAVAJARDIR%%/igv/commons-collections-20040616.jar
%%JAVAJARDIR%%/igv/commons-compress-1.19.jar
-%%JAVAJARDIR%%/igv/commons-configuration-1.10.jar
%%JAVAJARDIR%%/igv/commons-io-2.6.jar
%%JAVAJARDIR%%/igv/commons-jexl-2.1.1.jar
-%%JAVAJARDIR%%/igv/commons-lang-2.6.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/dsiutils-2.3.3.jar
%%JAVAJARDIR%%/igv/eventstream-1.0.1.jar
-%%JAVAJARDIR%%/igv/fastutil-7.0.12.jar
+%%JAVAJARDIR%%/igv/genomes/129S1_SvImJ.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/1kg_ref.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/1kg_v37.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/1kg_v37_alias.tab
+%%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.5.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.6.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/ABaumannii_ATCC_17978.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/ABaumannii_AYE_uid61637.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/AGPv3.31.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/ASM294v2.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/ASM985889v3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/AgamP3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/Aplysia.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/B73.chrom.sizes
@@ -48,6 +49,8 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/EBV_Type2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/Foxy4287.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/GCF_000233375.1.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/GCF_000364345.1.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/GCF_016920785.1.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/GSM552910.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/GSM552910_alias.tab
%%JAVAJARDIR%%/igv/genomes/Glamblia_2.0.chrom.sizes
@@ -114,10 +117,12 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/bosTau7.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/bosTau7_alias.tab
%%JAVAJARDIR%%/igv/genomes/bosTau8.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/bosTau9.chrom.sizes
%%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/canFam5.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/candida.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/cavPor3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/ce10.chrom.sizes
@@ -134,27 +139,34 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/dmel_5.9.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/dmel_r5.22.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/dmel_r5.33.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/dmel_r5.9.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/equCab2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/felCat5.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/galGal3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/galGal4.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/galGal5.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/galGal6.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/gasAcu1.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/gmax10.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/gmax8.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/gorGor4.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/gorGor6.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/hg16.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/hg17.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/hg18.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/hg19.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/hg19_alias.tab
%%JAVAJARDIR%%/igv/genomes/hg38.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/hg38_1kg.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/laevis_7.1.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/lmjr.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/lmjr_4.0.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/lmjr_4.0_alias.tab
+%%JAVAJARDIR%%/igv/genomes/macFas5_chrom.sizes
%%JAVAJARDIR%%/igv/genomes/me49.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/mg8.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/mm10.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/mm39.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/mm7.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/mm8.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/mm9.chrom.sizes
@@ -166,18 +178,23 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/osativa_6.1_alias.tab
%%JAVAJARDIR%%/igv/genomes/osativa_7.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/oviAri3.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/panPan2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/panTro2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/panTro3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/panTro4.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/panTro5.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/panTro6.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/ppatens_1.2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/pvivax.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/pvivax_alias.tab
+%%JAVAJARDIR%%/igv/genomes/rheMac10.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rheMac2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rheMac3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rheMac8.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rn4.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rn5.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/rn6.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/rn7.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/sacCer1.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/sacCer2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/sacCer2_alias.tab
@@ -192,6 +209,7 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/spur_2.1.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/spur_2.5.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/spur_3.0.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/susScr11.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/susScr3.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/susScrofa.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/taeGut1.chrom.sizes
@@ -210,54 +228,48 @@ bin/igv
%%JAVAJARDIR%%/igv/genomes/tcas_2.0.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/tcas_3.0.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/vvinifera.chrom.sizes
+%%JAVAJARDIR%%/igv/genomes/ws235.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/ws241.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/xenTro2.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/xenTro9.chrom.sizes
%%JAVAJARDIR%%/igv/genomes/zebrafish.chrom.sizes
-%%JAVAJARDIR%%/igv/goby-io-3.3.1.jar
%%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-2.15.67.jar
+%%JAVAJARDIR%%/igv/htsjdk-3.0.0.jar
+%%JAVAJARDIR%%/igv/http-client-spi-2.16.7.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-2.10.5.jar
-%%JAVAJARDIR%%/igv/jackson-core-2.10.5.jar
-%%JAVAJARDIR%%/igv/jackson-databind-2.10.5.1.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/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-2.15.67.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/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-4.1.53.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/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-2.15.67.jar
-%%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar
-%%JAVAJARDIR%%/igv/protocol-core-2.15.67.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-2.15.67.jar
-%%JAVAJARDIR%%/igv/s3-2.15.67.jar
-%%JAVAJARDIR%%/igv/sdk-core-2.15.67.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/slf4j-simple-1.7.26.jar
-%%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar
-%%JAVAJARDIR%%/igv/sts-2.15.67.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-2.15.67.jar
+%%JAVAJARDIR%%/igv/utils-2.16.7.jar
%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar
share/pixmaps/igv.png