update to 2.13.2

4 files changed, 59 insertions, 20 deletions

diff --git a/.SRCINFO b/.SRCINFO
index ecbdf69e1b88..d46fce216266 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,13 +1,16 @@
 pkgbase = igvtools
 	pkgdesc = IGV utilities for preprocessing bioinformatics data files
-	pkgver = 2.4.19
-	pkgrel = 2
+	pkgver = 2.13.2
+	pkgrel = 1
 	url = https://software.broadinstitute.org/software/igv
 	arch = any
-	license = GPL2
-	depends = java-runtime
-	depends = bash
-	source = http://data.broadinstitute.org/igv/projects/downloads/2.4/igvtools_2.4.19.zip
-	sha256sums = 7b351dde496ef9026b9da46f1962ce56b4a03ac04a212ddd59c3ba3caa9957c8
+	license = MIT
+	depends = java-runtime>=11
+	source = igvtools-2.13.2.zip::https://data.broadinstitute.org/igv/projects/downloads/2.13/IGV_2.13.2.zip
+	source = igvtools.sh
+	source = igvtools_gui.sh
+	sha256sums = 92ab783f693506cafc3499f014f63dce950534b0499e153853cde010a101c104
+	sha256sums = d4cda10928d773dbc959a1cd5bb336aeecf95cb5e549b4560ba561c66f27c50a
+	sha256sums = 1bf610102219c0390d7d78e993110e1cdcb5aae571a79cfa54b093ee3c50ff7f
 
 pkgname = igvtools
diff --git a/PKGBUILD b/PKGBUILD
index afc5ebe90dff..dc0b5d052471 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,25 +1,28 @@
 # Contributor: Clint Valentine <valentine.clint@gmail.com>
 # Maintainer: Stefan Husmann <stefan-husmann@t-online.de>
-
 pkgname=igvtools
-_pkgname=IGVTools
-pkgver=2.4.19
-pkgrel=2
+_pkgname=IGV
+pkgver=2.13.2
+pkgrel=1
 pkgdesc="IGV utilities for preprocessing bioinformatics data files"
 arch=('any')
 url="https://software.broadinstitute.org/software/igv"
-license=('GPL2')
-depends=('java-runtime' 'bash')
+license=('MIT')
+depends=('java-runtime>=11')
 source=(
-  http://data.broadinstitute.org/igv/projects/downloads/"${pkgver%.*}"/"${pkgname}"_"${pkgver}".zip
+  ${pkgname}-${pkgver}.zip::https://data.broadinstitute.org/igv/projects/downloads/${pkgver%.*}/IGV_${pkgver}.zip
+  "igvtools.sh"
+  "igvtools_gui.sh"
 )
-sha256sums=('7b351dde496ef9026b9da46f1962ce56b4a03ac04a212ddd59c3ba3caa9957c8')
+sha256sums=('92ab783f693506cafc3499f014f63dce950534b0499e153853cde010a101c104'
+            'd4cda10928d773dbc959a1cd5bb336aeecf95cb5e549b4560ba561c66f27c50a'
+            '1bf610102219c0390d7d78e993110e1cdcb5aae571a79cfa54b093ee3c50ff7f')
 
 package() {
-  install -Dm775 "${srcdir}"/${_pkgname}_${pkgver}/"${pkgname}" "${pkgdir}"/usr/bin/"${pkgname}"
-  install -Dm775 "${srcdir}"/${_pkgname}_${pkgver}/"${pkgname}_gui" "${pkgdir}"/usr/bin/"${pkgname}"_gui
-  install -Dm664 "${srcdir}"/${_pkgname}_${pkgver}/lib/"${pkgname}".jar \
-	  "${pkgdir}"/usr/share/java/igv/"${pkgname}".jar
+  install -d "${pkgdir}"/usr/share/java/igv/
+  cp -rf IGV_${pkgver}/lib/*  "${pkgdir}"/usr/share/java/igv/
   install -Dm644 "${srcdir}"/${_pkgname}_${pkgver}/igvtools_readme.txt \
 	  "${pkgdir}"/usr/share/doc/$pkgname/igvtools_readme.txt
+  install -Dm755 "igvtools.sh"  "${pkgdir}"/usr/bin/igvtools
+  install -Dm755 "igvtools_gui.sh"  "${pkgdir}"/usr/bin/igvtools_gui
 }
diff --git a/igvtools.sh b/igvtools.sh
index 7c1007886860..ec37ccd71a64 100644..100755
--- a/igvtools.sh
+++ b/igvtools.sh
@@ -1,2 +1,17 @@
 #!/bin/sh
-java -Djava.awt.headless=true -Xmx1500m -jar /usr/share/java/igv/igvtools.jar "${@}"
+java -Djava.awt.headless=true -Xmx1500m \
+    --add-exports java.desktop/com.sun.java.swing.plaf.windows=jide.common \
+    --add-exports java.desktop/javax.swing.plaf.synth=jide.common \
+    --add-exports java.desktop/sun.swing=jide.common \
+    --add-exports java.desktop/sun.awt=jide.common \
+    --add-exports java.desktop/sun.awt.image=jide.common \
+    --add-exports java.desktop/sun.awt.shell=jide.common \
+    --add-exports java.desktop/sun.awt.dnd=jide.common \
+    --add-exports java.desktop/sun.awt.windows=jide.common \
+    --add-exports java.base/sun.security.action=jide.common \
+    -Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize \
+    --module-path=/usr/share/java/igv \
+    --module=org.igv/org.broad.igv.tools.IgvTools "${@}"
+    # -jar /usr/share/java/igv/igv.jar
+
+# Disable a JAXB optimization that causes illegal access exceptions on Java 11
diff --git a/igvtools_gui.sh b/igvtools_gui.sh
new file mode 100755
index 000000000000..755b51a2d6f1
--- /dev/null
+++ b/igvtools_gui.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+java  -Xmx1500m \
+    --add-exports java.desktop/com.sun.java.swing.plaf.windows=jide.common \
+    --add-exports java.desktop/javax.swing.plaf.synth=jide.common \
+    --add-exports java.desktop/sun.swing=jide.common \
+    --add-exports java.desktop/sun.awt=jide.common \
+    --add-exports java.desktop/sun.awt.image=jide.common \
+    --add-exports java.desktop/sun.awt.shell=jide.common \
+    --add-exports java.desktop/sun.awt.dnd=jide.common \
+    --add-exports java.desktop/sun.awt.windows=jide.common \
+    --add-exports java.base/sun.security.action=jide.common \
+    -Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize \
+    -Dsun.java2d.uiScale=2 \
+    --module-path=/usr/share/java/igv \
+    --module=org.igv/org.broad.igv.tools.IgvTools gui "${@}"
+    # -jar /usr/share/java/igv/igv.jar
+
+# Disable a JAXB optimization that causes illegal access exceptions on Java 11