Mercurial > repos > peterjc > tmhmm_and_signalp
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
author | peterjc |
---|---|
date | Thu, 21 Sep 2017 11:35:20 -0400 |
parents | f3ecd80850e2 |
children | 238eae32483c |
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--- 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