diff tools/mira3/README.rst @ 16:f74bc0420db4 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643

--- a/tools/mira3/README.rst	Mon Apr 21 06:57:45 2014 -0400
+++ b/tools/mira3/README.rst	Wed May 13 05:45:01 2015 -0400
@@ -30,10 +30,15 @@
 * ``mira.xml`` (the Galaxy tool definition)
 
 The suggested location is a new ``tools/mira3`` folder. You will also need to
-modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
-this to ``tools_conf.xml.sample`` in order to run any tests::
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
+the line::
+ 
+  <tool file="mira3/mira.xml" />
 
-  <tool file="mira3/mira.xml" />
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    $ ./run_tests -id mira_assembler
 
 You will also need to install MIRA, we used version 3.4.1.1. See:
 
@@ -77,6 +82,8 @@
         - Correct path issue in automated dependency installation.
 v0.0.10 - Added a functional test.
         - Updated URL for automated installation of MIRA v3.4.1.1
+v0.0.11 - Tool definition now embeds citation information.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -89,21 +96,30 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
 
-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 mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+    ...
 
-Check this worked::
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+    ...
 
-    $ tar -tzf mira3_wrapper.tar.gz
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/mira3/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/empty_file.dat
+    test-data/tvc_contigs.fasta
+    test-data/tvc_mini.fastq
     tools/mira3/README.rst
-    tools/mira3/mira.xml
     tools/mira3/mira.py
+    tools/mira3/mira.xml
     tools/mira3/tool_dependencies.xml
-    test-data/tvc_mini.fastq
-    test-data/tvc_contigs.fasta
-    test-data/empty_file.dat
 
 
 Licence (MIT)