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comparison tools/protein_analysis/README.rst @ 30:6d9d7cdf00fc draft

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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 11:15:55 -0400
parents 3cb02adf4326
children 3c9bbbc6cbbe
comparison
equal deleted inserted replaced
29:3cb02adf4326 30:6d9d7cdf00fc
18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved. 19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
20 See the included LICENCE file for details (MIT open source licence). 20 See the included LICENCE file for details (MIT open source licence).
21 21
22 The wrappers are available from the Galaxy Tool Shed 22 The wrappers are available from the Galaxy Tool Shed
23 http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 23 http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
24 24
25 Citation 25 Citation
26 ======== 26 ========
27 27
28 If you use any of these Galaxy tools in work leading to a scientific 28 If you use any of these Galaxy tools in work leading to a scientific
172 - Use reStructuredText for this README file. 172 - Use reStructuredText for this README file.
173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. 174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
175 - Updated the ``suite_config.xml`` file (overdue). 175 - Updated the ``suite_config.xml`` file (overdue).
176 - Tool definition now embeds citation information. 176 - Tool definition now embeds citation information.
177 v0.2.7 - Style cleanup in Python scripts. 177 v0.2.7 - Style cleanup in Python scripts using ``pep8``.
178 v0.2.8 - Reorder XML elements (internal change only). 178 v0.2.8 - Reorder XML elements (internal change only).
179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
180 - Record version of Promoter 2 via ``<version_command>``. 180 - Record version of Promoter 2 via ``<version_command>``.
181 v0.2.9 - Further style cleanup in Python scripts (internal change only). 181 v0.2.9 - Further style cleanup in Python scripts (internal change only).
182 v0.2.10 - Style cleanup in Python scripts using ``flake8``.
183 - Record TMHMM and SignalP wrapper version via ``<version_command>``.
184 - Python 3 compatible print function and exception handling.
185 - Python 3 compatible subprocess calling.
186 - Removed obsolete ``suite_config.xml`` file.
187 v0.2.11 - Updated RXLR tool dependencies to get HMMER2 via BioConda.
188 - Use ``<command detect_errors="aggressive">`` (internal change only).
189 - Single quote command line arguments (internal change only).
190 - Record WoLF PSORT wrapper version via ``<version_command>``.
191 - Fix error handling in SignalP wrapper.
192 - Record SignalP version via ``<version_command>``.
193 - Internal job splitter will skip starting any pending jobs after a
194 child job fails (so the entire task will error out more quickly).
182 ======= ====================================================================== 195 ======= ======================================================================
183 196
184 197
185 Developers 198 Developers
186 ========== 199 ==========
195 208
196 For pushing a release to the test or main "Galaxy Tool Shed", use the following 209 For pushing a release to the test or main "Galaxy Tool Shed", use the following
197 Planemo commands (which requires you have set your Tool Shed access details in 210 Planemo commands (which requires you have set your Tool Shed access details in
198 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 211 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
199 212
200 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ 213 $ planemo shed_update -t testtoolshed --check_diff tools/protein_analysis/
201 ... 214 ...
202 215
203 or:: 216 or::
204 217
205 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/ 218 $ planemo shed_update -t toolshed --check_diff tools/protein_analysis/
206 ... 219 ...
207 220
208 To just build and check the tar ball, use:: 221 To just build and check the tar ball, use::
209 222
210 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/protein_analysis/ 223 $ planemo shed_upload --tar_only tools/protein_analysis/
211 ... 224 ...
212 $ tar -tzf shed_upload.tar.gz 225 $ tar -tzf shed_upload.tar.gz
213 test-data/Adenovirus.fasta 226 test-data/Adenovirus.fasta
214 test-data/Adenovirus.promoter2.tabular 227 test-data/Adenovirus.promoter2.tabular
215 test-data/empty.fasta 228 test-data/empty.fasta
216 test-data/empty_promoter2.tabular 229 test-data/empty_promoter2.tabular
217 test-data/empty_psortb_terse.tabular 230 test-data/empty_psortb_terse.tabular