# HG changeset patch
# User peterjc
# Date 1416482149 18000
# Node ID 4d9a4a43861b190f38ed8754c2b048e33a932055
# Parent 6a9debe4b860ac595b3d7c08d2aeb02f3df6bfd1
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/README.rst
--- a/tools/clinod/README.rst Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/README.rst Thu Nov 20 06:15:49 2014 -0500
@@ -18,35 +18,36 @@
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 $CLINOD to their folder.
+Neural Network Simulator (SNNS), and set the ``$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 $CLINOD/clinod-1.3.jar which means if you used
-/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
+to access command line NoD as ``$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 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
+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:
+folder, e.g. in a ``tools/clinod`` folder:
-* clinod.xml (the Galaxy tool definition)
-* README.rst (this file)
+* ``clinod.xml`` (the Galaxy tool definition)
+* ``README.rst`` (this file)
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
tool. If you are using other protein analysis tools like TMHMM or SignalP, put
it next to them. Just add the line::
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
- $ ./run_functional_tests.sh -id clinod
+ $ ./run_tests.sh -id clinod
That's it.
@@ -67,6 +68,8 @@
- Use reStructuredText for this README file.
- Updated citation information (Cock et al. 2013).
- Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.7 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
+ - Tool definition now embeds citation information.
======= ======================================================================
diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/clinod.xml Thu Nov 20 06:15:49 2014 -0500
@@ -1,4 +1,4 @@
-
+Find nucleolar localization signals (NoLSs) in protein sequencesjava
@@ -7,8 +7,7 @@
##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="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
-##I want the number of threads to be a Galaxy config option...
+java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
##TODO - Make the -clean_sequence argument a parameter?
@@ -25,7 +24,7 @@
-
+
@@ -82,4 +81,9 @@
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
+
+ 10.7717/peerj.167
+ 10.1093/nar/gkq653
+ 10.1186/1471-2105-12-317
+
diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/tool_dependencies.xml
--- a/tools/clinod/tool_dependencies.xml Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/tool_dependencies.xml Thu Nov 20 06:15:49 2014 -0500
@@ -9,7 +9,7 @@
wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz
- tar -zxvf SNNSv4.3.tar.gz
+ tar -zxvf SNNSv4.3.tar.gz$INSTALL_DIR/wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar