Mercurial > repos > peterjc > tmhmm_and_signalp
comparison 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 |
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date | Thu, 21 Sep 2017 11:35:20 -0400 |
parents | f3ecd80850e2 |
children | 238eae32483c |
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19:f3ecd80850e2 | 20:a19b3ded8f33 |
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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 |