naked-singularity-v0.9.0 :: explicitly set java to version 1.8.0 instead

of the 'latest' version in both beast-gpu.def and beast2-gpu.def for
comet; set explicit path to figtree lib directory in launcher script and
made this script executable, which it was not by default

README

@@ -46,8 +46,8 @@ AUTHOR
 
 VERSION
 
-    0.8.9
+    0.9.0
 
 LAST UPDATED
 
-    Thursday, February 6th, 2020
+    Monday, February 10th, 2020

definition-files/comet/beast/beast-gpu.def

@@ -15,7 +15,7 @@ Include: yum
     AUTHOR_NAME Marty Kandes
     AUTHOR_EMAIL mkandes@sdsc.edu
 
-    LAST_UPDATED 20200205
+    LAST_UPDATED 20200209
 
 %setup
 
@@ -129,8 +129,8 @@ Include: yum
     yum -y install libXi-devel
     yum -y install mesa-libGLU
     yum -y install mesa-libGLU-devel
-    yum -y install java-latest-openjdk
-    yum -y install java-latest-openjdk-devel
+    yum -y install java-1.8.0-openjdk
+    yum -y install java-1.8.0-openjdk-devel
 
     yum -y install grubby
     yum -y install libtirpc
@@ -386,6 +386,9 @@ Include: yum
     sed -i 's/linux_unix_Release/linux/g' build.xml
     ant linux
     mv /tmp/figtree/release/Linux/FigTree_v1.4.4 /opt/figtree
+    cd /opt/figtree/bin
+    sed -i "s/lib/\/opt\/figtree\/lib/g" figtree
+    chmod +x figtree
 
     # Set PATH to figtree
     export PATH="/opt/figtree/bin:${PATH}" 

definition-files/comet/beast2/beast2-gpu.def

@@ -15,7 +15,7 @@ Include: yum
     AUTHOR_NAME Marty Kandes
     AUTHOR_EMAIL mkandes@sdsc.edu
 
-    LAST_UPDATED 20200206
+    LAST_UPDATED 20200208
 
 %setup
 
@@ -129,8 +129,8 @@ Include: yum
     yum -y install libXi-devel
     yum -y install mesa-libGLU
     yum -y install mesa-libGLU-devel
-    yum -y install java-latest-openjdk
-    yum -y install java-latest-openjdk-devel
+    yum -y install java-1.8.0-openjdk
+    yum -y install java-1.8.0-openjdk-devel
 
     yum -y install grubby
     yum -y install libtirpc
@@ -386,6 +386,9 @@ Include: yum
     sed -i 's/linux_unix_Release/linux/g' build.xml
     ant linux
     mv /tmp/figtree/release/Linux/FigTree_v1.4.4 /opt/figtree
+    cd /opt/figtree/bin
+    sed -i "s/lib/\/opt\/figtree\/lib/g" figtree
+    chmod +x figtree
 
     # Set PATH to figtree
     export PATH="/opt/figtree/bin:${PATH}"