From 78e89143d43ae02aea1ff0359dbbd755e409c95f Mon Sep 17 00:00:00 2001
From: scalavision <scalavison@gmail.com>
Date: Wed, 26 Feb 2020 14:42:47 +0100
Subject: [PATCH] igv: 2.4.19 -> 2.8.9

Co-Authored-By: Silvan Mosberger <contact@infinisil.com>
---
 .../science/biology/igv/default.nix           | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix
index 04699a84b69..33f21b208d9 100644
--- a/pkgs/applications/science/biology/igv/default.nix
+++ b/pkgs/applications/science/biology/igv/default.nix
@@ -1,32 +1,34 @@
-{ stdenv, fetchurl, unzip, jre }:
+{ stdenv, fetchzip, jdk11 }:
 
 stdenv.mkDerivation rec {
   pname = "igv";
-  version = "2.4.19";
-
-  src = fetchurl {
-    url = "https://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip";
-    sha256 = "048dgrhxcb854d24kyjkqz12bw04bsv49i5jawb75yzkswwfkb0z";
+  version = "2.8.9";
+  src = fetchzip {
+    url = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_${version}.zip";
+    sha256 = "1874w1xprv91caz1ymfxilq6inhj36xzx8j9m0mcyp0qfvfvyjp7";
   };
 
-  buildInputs = [ unzip jre ];
-
   installPhase = ''
     mkdir -pv $out/{share,bin}
     cp -Rv * $out/share/
 
     sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh
-    sed -i 's#java#${jre}/bin/java#g' $out/share/igv.sh
+    sed -i 's#java#${jdk11}/bin/java#g' $out/share/igv.sh
+
+    sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igvtools
+    sed -i 's#java#${jdk11}/bin/java#g' $out/share/igvtools
 
     ln -s $out/share/igv.sh $out/bin/igv
+    ln -s $out/share/igvtools $out/bin/igvtools
 
     chmod +x $out/bin/igv
+    chmod +x $out/bin/igvtools
   '';
 
   meta = with stdenv.lib; {
     homepage = https://www.broadinstitute.org/igv/;
     description = "A visualization tool for interactive exploration of genomic datasets";
-    license = licenses.lgpl21;
+    license = licenses.mit;
     platforms = platforms.unix;
     maintainers = [ maintainers.mimame ];
   };