diff tools/mummer/README.rst @ 4:5f5a358b281f draft

v0.0.5 internal changes
author peterjc
date Wed, 05 Aug 2015 11:34:31 -0400
parents 154c000d3fef
children 683ea5ab0008
line wrap: on
line diff
--- a/tools/mummer/README.rst	Thu Nov 06 11:50:19 2014 -0500
+++ b/tools/mummer/README.rst	Wed Aug 05 11:34:31 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for drawing dotplots using MUMmer 3
 ==================================================
 
-This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -43,8 +43,8 @@
 
   <tool file="mummer/mummer.xml" />
 
-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_tests.sh -id mummerplot_wrapper
 
@@ -63,6 +63,8 @@
 v0.0.3  - Install ``ps2pdf`` using Tool Shed's GhostScript package.
 v0.0.4  - Install ``gnuplot`` using Tool Shed's gnuplot package.
         - Test case added.
+v0.0.5  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -72,22 +74,32 @@
 Development is on GitHub at:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ tar -czf mummer.tar.gz tools/mummer/README.rst tools/mummer/mummer.xml tools/mummer/mummer.py tools/mummer/tool_dependencies.xml test-data/magic.png test-data/magic.pdf test-data/rhodopsin_nucs.fasta test-data/three_human_mRNA.fasta
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
+    ...
 
-Check this worked::
+or::
 
-    $ tar -tzf mummer.tar.gz
-    tools/mummer/README.rst
-    tools/mummer/mummer.xml
-    tools/mummer/mummer.py
-    tools/mummer/tool_dependencies.xml
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/mummer/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/magic.pdf
     test-data/magic.png
-    test-data/magic.pdf
     test-data/rhodopsin_nucs.fasta
     test-data/three_human_mRNA.fasta
+    tools/mummer/README.rst
+    tools/mummer/mummer.py
+    tools/mummer/mummer.xml
+    tools/mummer/tool_dependencies.xml
 
 
 Licence (MIT)