diff tools/protein_analysis/README.rst @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

--- a/tools/protein_analysis/README.rst	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/README.rst	Thu Sep 21 11:35:20 2017 -0400
@@ -20,7 +20,7 @@
 See the included LICENCE file for details (MIT open source licence).
 
 The wrappers are available from the Galaxy Tool Shed
-http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 
+http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
 
 Citation
 ========
@@ -174,11 +174,24 @@
 v0.2.6  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
         - Updated the ``suite_config.xml`` file (overdue).
         - Tool definition now embeds citation information.
-v0.2.7  - Style cleanup in Python scripts.
+v0.2.7  - Style cleanup in Python scripts using ``pep8``.
 v0.2.8  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - Record version of Promoter 2 via ``<version_command>``.
 v0.2.9  - Further style cleanup in Python scripts (internal change only).
+v0.2.10 - Style cleanup in Python scripts using ``flake8``.
+        - Record TMHMM and SignalP wrapper version via ``<version_command>``.
+        - Python 3 compatible print function and exception handling.
+        - Python 3 compatible subprocess calling.
+        - Removed obsolete ``suite_config.xml`` file.
+v0.2.11 - Updated RXLR tool dependencies to get HMMER2 via BioConda.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+        - Record WoLF PSORT wrapper version via ``<version_command>``.
+        - Fix error handling in SignalP wrapper.
+        - Record SignalP version via ``<version_command>``.
+        - Internal job splitter will skip starting any pending jobs after a
+          child job fails (so the entire task will error out more quickly).
 ======= ======================================================================
 
 
@@ -197,19 +210,19 @@
 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)::
 
-    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
+    $ planemo shed_update -t testtoolshed --check_diff tools/protein_analysis/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
+    $ planemo shed_update -t toolshed --check_diff tools/protein_analysis/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/protein_analysis/
+    $ planemo shed_upload --tar_only tools/protein_analysis/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/Adenovirus.fasta
     test-data/Adenovirus.promoter2.tabular
     test-data/empty.fasta