sage: fix jmol integration

pkgs/applications/science/math/sage/env-locations.nix

@@ -39,7 +39,7 @@ writeTextFile rec {
     export ECLDIR='${ecl}/lib/ecl-${ecl.version}/'
     export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
     export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"
-    export JMOL_DIR="${jmol}"
+    export JMOL_DIR="${jmol}/share/jmol" # point to the directory that contains JmolData.jar
     export JSMOL_DIR="${jmol}/share/jsmol"
     export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax"
     export THREEJS_DIR="${three}/lib/node_modules/three"

pkgs/applications/science/math/sage/sage-env.nix

@@ -44,6 +44,7 @@
 , zlib
 , gsl
 , ntl
+, jdk
 }:
 
 # This generates a `sage-env` shell file that will be sourced by sage on startup.
@@ -91,6 +92,7 @@ let
     lcalc
     rubiks
     flintqs
+    jdk # only needed for `jmol` which may be replaced in the future
   ]
   ));
 in