# HG changeset patch
# User peterjc
# Date 1367936997 14400
# Node ID 3213023deae162d079ad8660453c39bf7f9018b3
# Parent  a4881144d6f4c2a3e677f1c769430232c0e1de7b
Uploaded v0.0.5 take 2, attempt auto-installation

diff -r a4881144d6f4 -r 3213023deae1 tools/clinod/clinod.txt
--- a/tools/clinod/clinod.txt	Thu May 02 12:53:42 2013 -0400
+++ b/tools/clinod/clinod.txt	Tue May 07 10:29:57 2013 -0400
@@ -13,15 +13,23 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
 
 
-Installation
-============
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
+Neural Network Simulator (SNNS), and set the $CLINOD to their folder.
+
+
+Manual Installation
+===================
 This wrapper expects the java binary to be on the system PATH, and to be able
-to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if
-you wish to use a different location).
+to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
+/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
 
-Internally NoD calls the binary batchman from the Stuttgart Neural Network
-Simulator (SNNS) v 4.2 software suite. This binary can either be on the system
-path or located next to the JAR file, i.e. /opt/clinod/batchman
+Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
+Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
+system path or located next to the JAR file, i.e. /opt/clinod/batchman
 
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a tools/clinod folder:
@@ -51,7 +59,7 @@
 v0.0.3 - Describe output table in help
 v0.0.4 - Added unit test
 v0.0.5 - Link to Tool Shed added to help text and this documentation.
-       - Moved files pending automated tool installation.
+       - Automated tool installation.
 
 
 Developers
diff -r a4881144d6f4 -r 3213023deae1 tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Thu May 02 12:53:42 2013 -0400
+++ b/tools/clinod/clinod.xml	Tue May 07 10:29:57 2013 -0400
@@ -1,9 +1,15 @@
 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
+    <requirements>
+        <requirement type="binary">java</requirement>
+        <requirement type="package" version="1.3">clinod</requirement>
+    </requirements>
     <command>
-      java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
-      ##I want the number of threads to be a Galaxy config option...
-      ##TODO - Make the -clean_sequence argument a parameter?
+##The Galaxy Tool Shed installation should define $CLINOD to point at folder
+##containing both clinod-1.3.jar and the batchman binary:
+java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
+##I want the number of threads to be a Galaxy config option...
+##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <stdio>
         <!-- Assume anything other than zero is an error -->
@@ -16,9 +22,6 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="NoD results" />
     </outputs>
-    <requirements>
-        <requirement type="binary">java</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />