From 4d201589fe87637355a5f74a6c030824e0a38e75 Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Mon, 10 Feb 2020 22:30:58 +0000
Subject: [PATCH] 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 | 4 ++--
definition-files/comet/beast/beast-gpu.def | 9 ++++++---
definition-files/comet/beast2/beast2-gpu.def | 9 ++++++---
3 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/README b/README
index e499a41..0cf47b3 100644
--- a/README
+++ b/README
@@ -46,8 +46,8 @@ AUTHOR
VERSION
- 0.8.9
+ 0.9.0
LAST UPDATED
- Thursday, February 6th, 2020
+ Monday, February 10th, 2020
diff --git a/definition-files/comet/beast/beast-gpu.def b/definition-files/comet/beast/beast-gpu.def
index 8ccec90..a7a320e 100644
--- a/definition-files/comet/beast/beast-gpu.def
+++ b/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:${PATH}"
diff --git a/definition-files/comet/beast2/beast2-gpu.def b/definition-files/comet/beast2/beast2-gpu.def
index 24401aa..16d9849 100644
--- a/definition-files/comet/beast2/beast2-gpu.def
+++ b/definition-files/comet/beast2/beast2-gpu.def
@@ -15,7 +15,7 @@ Include: yum
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
- LAST_UPDATED 20200206
+ LAST_UPDATED 20200208
%setup
@@ -129,8 +129,8 @@ Include: yum
yum -y install libXi-devel
yum -y install mesa-libGLU
yum -y install mesa-libGLU-devel
- yum -y install java-latest-openjdk
- yum -y install java-latest-openjdk-devel
+ yum -y install java-1.8.0-openjdk
+ yum -y install java-1.8.0-openjdk-devel
yum -y install grubby
yum -y install libtirpc
@@ -386,6 +386,9 @@ Include: yum
sed -i 's/linux_unix_Release/linux/g' build.xml
ant linux
mv /tmp/figtree/release/Linux/FigTree_v1.4.4 /opt/figtree
+ cd /opt/figtree/bin
+ sed -i "s/lib/\/opt\/figtree\/lib/g" figtree
+ chmod +x figtree
# Set PATH to figtree
export PATH="/opt/figtree/bin:${PATH}"
--
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