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-rw-r--r--PKGBUILD41
-rw-r--r--igv.desktop7
-rw-r--r--igv.sh6
-rw-r--r--igv_hidpi.desktop12
-rw-r--r--igv_hidpi.sh11
5 files changed, 54 insertions, 23 deletions
diff --git a/PKGBUILD b/PKGBUILD
index de069bbe541..e94a13e2205 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -3,32 +3,35 @@
# Maintainer: Piotr Balwierz <parseByHuman(surname at email_service_of_google)>
pkgname=igv
-pkgver=2.4.11
-_pkgver=${pkgver//_/-}
-pkgrel=2
-pkgdesc="High-performance visualization tool for interactive exploration of large, integrated genomic datasets."
+pkgver=2.5.1
+_pkgver=${pkgver//_/-} # currently not needed
+pkgrel=1
+pkgdesc="High-performance visualization tool for interactive exploration of large, integrated genomic datasets. From Broad Institute."
arch=('any')
url="http://www.broadinstitute.org/software/igv/home"
license=('LGPL')
-depends=('java-environment=8' 'archlinux-java-run' 'sh')
+depends=('jre-openjdk' 'archlinux-java-run' 'sh')
#"igv-$pkgver.tar.gz::https://github.com/igvteam/igv/archive/v$pkgver.tar.gz"
-source=("http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_$pkgver.zip"
- "http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/tools.png"
+source=("http://data.broadinstitute.org/igv/projects/downloads/2.5/IGV_Linux_$pkgver.zip"
+ #"http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/tools.png"
"$pkgname.sh"
- "$pkgname.desktop")
-sha512sums=('d3f7c0e3a4b090fe3ae1d21375be0285c026dcf284fdefdaa02bd0247bd27515e9c2dc14798ebad2f0273bd70bbdad2aaff3dc91ecfd9cc74993246ae0b10a98'
- 'e71a0dc70c717b3db00268632500b5723b8cddb1ecfbd8ce48b77ffad59bf93a8d275cc5ebd18b9eb1025200438ac55ec348def343b1b5f72a2c982b5dc4cc90'
- '1f0cdbb8467de2a4b287da3fc366f8b5b967f744dab28ffb613a88257caa326b7a1332c8b656ec8fd69ef00114a8d658db6a73fde89b55e7918be094cc6f56ff'
- '5ba8666c9c0568f11baf79242c4853964a4061269c0b84529b71a02a106e142bc559ccb97a6a51801dbccacf5f2061cead315b5ece60fc4564c3c38b02d733e7')
+ "igv_hidpi.sh"
+ "$pkgname.desktop"
+ "igv_hidpi.desktop")
+sha512sums=('7933b20d7e06b9c50f8bae9ecc8dd0e9723b887576bb2ccf50358cc53e7ffac19990a79f2ee4f8e6e8b7dbc7e298c037ce8e9781cc8179c7ca7ef1f5ac985d41'
+ #'e71a0dc70c717b3db00268632500b5723b8cddb1ecfbd8ce48b77ffad59bf93a8d275cc5ebd18b9eb1025200438ac55ec348def343b1b5f72a2c982b5dc4cc90'
+ '70de493d5188d6eedbd0bf7c74d41ce4829efab75e3a79b56f998326c209d0184f5d3624d6b85d01ad93f0462e785c314322ef4a9260ead6d747f1791ecbe649'
+ '60c9c8c6f66259a4edafd1d58d1f1ebcda4450f7620d4c0fc987d5875c2fd531bc2a3159fcdb77975bf07002036e3544f4d301a31d1085ab24d576eea1f8adcb'
+ 'c6bd4fc8bb7e43ee0fe9a4709e716d015c678bdd8bcb897876c267ec48441e2383aebb26b80457d2238f79546537af3409aa698544dc0043ff2c921f18126662'
+ '0d52cbd6adc2bf36f8b80acdb6d72b30d52e920b301e7af75ddee8d942c9f3467f7aa98129984ee269c6aaaacc703fb054ba2917e0d7dbce5620050623383e5b')
package() {
install -Dm755 $pkgname.sh "$pkgdir"/usr/bin/$pkgname
- install -Dm644 tools.png "$pkgdir"/usr/share/pixmaps/$pkgname.png
+ install -Dm755 "$pkgname"_hidpi.sh "$pkgdir"/usr/bin/"$pkgname"_hidpi
install -Dm644 $pkgname.desktop "$pkgdir"/usr/share/applications/$pkgname.desktop
- cd IGV_${_pkgver}
- install -Dm644 $pkgname.jar "$pkgdir"/usr/share/java/$pkgname/$pkgname.jar
- install -Dm644 batik-codec__V1.7.jar \
- "$pkgdir"/usr/share/java/$pkgname/batik-codec__V1.7.jar
- install -Dm644 goby-io-igv__V1.0.jar \
- "$pkgdir"/usr/share/java/$pkgname/goby-io-igv__V1.0.jar
+ install -Dm644 "$pkgname"_hidpi.desktop "$pkgdir"/usr/share/applications/"$pkgname"_hidpi.desktop
+ cd IGV_Linux_${_pkgver}
+ install -Dm644 IGV_64.png "$pkgdir"/usr/share/pixmaps/$pkgname.png
+ install -Dm644 igv.args "$pkgdir"/usr/share/java/$pkgname/igv.args
+ install -Dm644 lib/* -t "$pkgdir"/usr/share/java/$pkgname/lib/
}
diff --git a/igv.desktop b/igv.desktop
index bbf7ab91071..650f95241c2 100644
--- a/igv.desktop
+++ b/igv.desktop
@@ -1,8 +1,11 @@
[Desktop Entry]
Type=Application
-Version=2.4.11
+Version=2.5.1
Name=IGV
-Comment=Integrative Genomics Viewer
+GenericName=Integrative Genomics Viewer
+X-GNOME-FullName=Integrative Genomics Viewer
+Comment=Integrative Genomics Viewer (Broad Institute)
+Keywords=genome;
Exec=igv
Icon=igv
Terminal=false
diff --git a/igv.sh b/igv.sh
index 3b2851da6f1..be7678031e5 100644
--- a/igv.sh
+++ b/igv.sh
@@ -1,8 +1,10 @@
#!/bin/sh
LANG=C phymem=$(free -m | awk '/^Mem:/{print $2}')
igvmem=$(($phymem / 3))
-archlinux-java-run --min 8 --max 8 -- \
+archlinux-java-run --min 11 --max 11 -- \
-Xmx${igvmem}m \
+ @"/usr/share/java/igv/igv.args" \
-Dapple.laf.useScreenMenuBar=true \
-Djava.net.preferIPv4Stack=true \
- -jar /usr/share/java/igv/igv.jar
+ --module-path=/usr/share/java/igv/lib \
+ --module=org.igv/org.broad.igv.ui.Main "$@"
diff --git a/igv_hidpi.desktop b/igv_hidpi.desktop
new file mode 100644
index 00000000000..3b48eb4c145
--- /dev/null
+++ b/igv_hidpi.desktop
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Type=Application
+Version=2.5.1
+Name=IGV (High Resolution Screen mode)
+GenericName=Integrative Genomics Viewer
+X-GNOME-FullName=Integrative Genomics Viewer
+Comment=Integrative Genomics Viewer (Broad Institute)
+Keywords=genome;
+Exec=igv_hidpi
+Icon=igv
+Terminal=false
+Categories=Science
diff --git a/igv_hidpi.sh b/igv_hidpi.sh
new file mode 100644
index 00000000000..42e91be9932
--- /dev/null
+++ b/igv_hidpi.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+LANG=C phymem=$(free -m | awk '/^Mem:/{print $2}')
+igvmem=$(($phymem / 3))
+archlinux-java-run --min 11 --max 11 -- \
+ -Xmx${igvmem}m \
+ @"/usr/share/java/igv/igv.args" \
+ -Dapple.laf.useScreenMenuBar=true \
+ -Djava.net.preferIPv4Stack=true \
+ -Dsun.java2d.uiScale=2 \
+ --module-path=/usr/share/java/igv/lib \
+ --module=org.igv/org.broad.igv.ui.Main "$@"