diff tools/clinod/README.rst @ 8:4863b1dbe8f0 draft

"Update all the pico_galaxy tools on main Tool Shed"

--- a/tools/clinod/README.rst	Tue May 16 08:50:43 2017 -0400
+++ b/tools/clinod/README.rst	Fri Apr 16 22:33:30 2021 +0000
@@ -23,10 +23,11 @@
 
 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``
+This wrapper expects the java binary to availabe via a wapper script named
+``clinod`` on the system ``$PATH``.
+
+Older versions of this tool called the JAR file directly via an environment
+variable as ``$CLINOD/clinod-1.3.jar`` - this is no longer used.
 
 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
@@ -75,6 +76,11 @@
 v0.0.9  - Explicitly record clinod version via ``<version_command>``.
 v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
+v0.1.0  - Calls the JAR file via a wrapper script ``clinod``, in order to use
+          the BioConda package OR the ``tool_dependencies.xml`` system.
+          To do this the Tool Shed XML installation recipe now installs the
+          same wrapper script ``clinod`` used in the BioConda package for
+          calling the JAR file.
 ======= ======================================================================
 
 
@@ -103,7 +109,7 @@
 
     $ planemo shed_upload --tar_only tools/clinod/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/four_human_proteins.fasta
     test-data/four_human_proteins.clinod-1.3.tabular
     tools/clinod/README.rst