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comparison tools/protein_analysis/README.rst @ 26:20139cb4c844 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
author peterjc
date Wed, 13 May 2015 06:14:42 -0400
parents 41a42022f815
children 9e36a1b9302d
comparison
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25:41a42022f815 26:20139cb4c844
12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally. 12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
13 13
14 To use these Galaxy wrappers you must first install the command line tools. 14 To use these Galaxy wrappers you must first install the command line tools.
15 At the time of writing they are all free for academic use, or open source. 15 At the time of writing they are all free for academic use, or open source.
16 16
17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute 17 These wrappers are copyright 2010-2015 by Peter Cock, James Hutton Institute
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
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.
178 v0.2.8 - Reorder XML elements (internal change only).
179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
177 ======= ====================================================================== 180 ======= ======================================================================
178 181
179 182
180 Developers 183 Developers
181 ========== 184 ==========
185 http://bitbucket.org/peterjc/galaxy-central/src/tools 188 http://bitbucket.org/peterjc/galaxy-central/src/tools
186 189
187 Development has now moved to a dedicated GitHub repository: 190 Development has now moved to a dedicated GitHub repository:
188 https://github.com/peterjc/pico_galaxy/tree/master/tools 191 https://github.com/peterjc/pico_galaxy/tree/master/tools
189 192
190 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 193
191 the following command from the Galaxy root folder:: 194 For pushing a release to the test or main "Galaxy Tool Shed", use the following
192 195 Planemo commands (which requires you have set your Tool Shed access details in
193 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh 196 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
197
198 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
199 ...
200
201 or::
202
203 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
204 ...
205
206 To just build and check the tar ball, use::
207
208 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/protein_analysis/
209 ...
210 $ tar -tzf shed_upload.tar.gz
211 test-data/Adenovirus.fasta
212 test-data/Adenovirus.promoter2.tabular
213 test-data/empty.fasta
214 test-data/empty_promoter2.tabular
215 test-data/empty_psortb_terse.tabular
216 test-data/empty_rxlr.Bhattacharjee2006.tabular
217 test-data/empty_rxlr.Whisson2007.tabular
218 test-data/empty_rxlr.Win2007.tabular
219 test-data/empty_signalp3.tabular
220 test-data/empty_tmhmm2.tabular
221 test-data/empty_wolf_psort.tabular
222 test-data/four_human_proteins.fasta
223 test-data/four_human_proteins.signalp3.tabular
224 test-data/four_human_proteins.tmhmm2.tabular
225 test-data/four_human_proteins.wolf_psort.tabular
226 test-data/k12_ten_proteins.fasta
227 test-data/k12_ten_proteins_psortb_p_terse.tabular
228 test-data/rxlr_win_et_al_2007.fasta
229 test-data/rxlr_win_et_al_2007.tabular
230 test-data/rxlr_win_et_al_2007_sp3.tabular
231 tools/protein_analysis/LICENSE.txt
232 tools/protein_analysis/README.rst
233 tools/protein_analysis/promoter2.py
234 tools/protein_analysis/promoter2.xml
235 tools/protein_analysis/psortb.py
236 tools/protein_analysis/psortb.xml
237 tools/protein_analysis/rxlr_motifs.py
238 tools/protein_analysis/rxlr_motifs.xml
239 tools/protein_analysis/seq_analysis_utils.py
240 tools/protein_analysis/signalp3.py
241 tools/protein_analysis/signalp3.xml
242 tools/protein_analysis/suite_config.xml
243 tools/protein_analysis/tmhmm2.py
244 tools/protein_analysis/tmhmm2.xml
245 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
246 tools/protein_analysis/wolf_psort.py
247 tools/protein_analysis/wolf_psort.xml
194 248
195 This simplifies ensuring a consistent set of files is bundled each time, 249 This simplifies ensuring a consistent set of files is bundled each time,
196 including all the relevant test files. 250 including all the relevant test files.