[med-svn] [prottest] 02/03: Explain missing features in README.Debian

[Andreas Tille]

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tille pushed a commit to branch master
in repository prottest.

commit e03222b5b1cd858fd7555fe26c0c9664203eb2c5
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 19 16:21:15 2015 +0200

    Explain missing features in README.Debian
---
 debian/README.Debian       | 18 ++++++++++++++++++
 debian/bin/mpjrun.sh       |  6 +++++-
 debian/bin/runXProtTestHPC | 17 +++++++++++++++--
 3 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..fac4d92
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,18 @@
+Prottest for Debian
+===================
+
+Prottest3 was originally packaged as a predependency for jmodeltest
+(https://github.com//ddarriba/jmodeltest2).  The following Prottest3
+features are not yet implemented inside the prottest package but might
+be added at user request:
+
+  1. Parallel version:
+     To enable this it seems libmpj-java needs to feature starter.jar
+     which is not yet the case.
+
+  2. GUI
+     It seems prottest makes use of some netbeans features.  This needs
+     to be sorted out at request.
+
+
+ -- Andreas Tille <tille at debian.org>  Fri, 16 Oct 2015 23:38:00 +0200
diff --git a/debian/bin/mpjrun.sh b/debian/bin/mpjrun.sh
index ecd9df0..7bbfbe4 100755
--- a/debian/bin/mpjrun.sh
+++ b/debian/bin/mpjrun.sh
@@ -1,2 +1,6 @@
-#!/bin/sh 
+#!/bin/sh
+
+echo "Debian package libmpj-java does not contain starter.jar"
+exit
+
 java -jar $MPJ_HOME/lib/starter.jar "$@"	  
diff --git a/debian/bin/runXProtTestHPC b/debian/bin/runXProtTestHPC
index f5e3888..a71f708 100755
--- a/debian/bin/runXProtTestHPC
+++ b/debian/bin/runXProtTestHPC
@@ -1,2 +1,15 @@
-#!/bin/sh
-java -cp prottest-3.4.jar es.uvigo.darwin.xprottest.XProtTestApp
+#! /bin/sh
+
+echo "The GUI seems to need some components from netbeans."
+exit
+
+set -e
+
+# export JAVA_HOME=/usr/lib/jvm/default-java
+export JAVA_CMD=java
+export PROTTEST_HOME=/usr/share/prottest
+
+# Include the wrappers utility script
+. /usr/lib/java-wrappers/java-wrappers.sh
+
+run_java -Xms128M -Xmx1G -cp /usr/share/prottest/prottest.jar es.uvigo.darwin.xprottest.XProtTestApp "$@"

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