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comparison tools/protein_analysis/README.rst @ 18:eb6ac44d4b8e draft

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Suite v0.2.8, record Promoter 2 verion + misc internal updates
author peterjc
date Tue, 01 Sep 2015 09:56:36 -0400
parents e6cc27d182a8
children f3ecd80850e2
comparison
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17:e6cc27d182a8 18:eb6ac44d4b8e
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).
180 - Record version of Promoter 2 via ``<version_command>``.
177 ======= ====================================================================== 181 ======= ======================================================================
178 182
179 183
180 Developers 184 Developers
181 ========== 185 ==========
185 http://bitbucket.org/peterjc/galaxy-central/src/tools 189 http://bitbucket.org/peterjc/galaxy-central/src/tools
186 190
187 Development has now moved to a dedicated GitHub repository: 191 Development has now moved to a dedicated GitHub repository:
188 https://github.com/peterjc/pico_galaxy/tree/master/tools 192 https://github.com/peterjc/pico_galaxy/tree/master/tools
189 193
190 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 194
191 the following command from the Galaxy root folder:: 195 For pushing a release to the test or main "Galaxy Tool Shed", use the following
192 196 Planemo commands (which requires you have set your Tool Shed access details in
193 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh 197 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
198
199 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
200 ...
201
202 or::
203
204 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
205 ...
206
207 To just build and check the tar ball, use::
208
209 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/protein_analysis/
210 ...
211 $ tar -tzf shed_upload.tar.gz
212 test-data/Adenovirus.fasta
213 test-data/Adenovirus.promoter2.tabular
214 test-data/empty.fasta
215 test-data/empty_promoter2.tabular
216 test-data/empty_psortb_terse.tabular
217 test-data/empty_rxlr.Bhattacharjee2006.tabular
218 test-data/empty_rxlr.Whisson2007.tabular
219 test-data/empty_rxlr.Win2007.tabular
220 test-data/empty_signalp3.tabular
221 test-data/empty_tmhmm2.tabular
222 test-data/empty_wolf_psort.tabular
223 test-data/four_human_proteins.fasta
224 test-data/four_human_proteins.signalp3.tabular
225 test-data/four_human_proteins.tmhmm2.tabular
226 test-data/four_human_proteins.wolf_psort.tabular
227 test-data/k12_ten_proteins.fasta
228 test-data/k12_ten_proteins_psortb_p_terse.tabular
229 test-data/rxlr_win_et_al_2007.fasta
230 test-data/rxlr_win_et_al_2007.tabular
231 test-data/rxlr_win_et_al_2007_sp3.tabular
232 tools/protein_analysis/LICENSE.txt
233 tools/protein_analysis/README.rst
234 tools/protein_analysis/promoter2.py
235 tools/protein_analysis/promoter2.xml
236 tools/protein_analysis/psortb.py
237 tools/protein_analysis/psortb.xml
238 tools/protein_analysis/rxlr_motifs.py
239 tools/protein_analysis/rxlr_motifs.xml
240 tools/protein_analysis/seq_analysis_utils.py
241 tools/protein_analysis/signalp3.py
242 tools/protein_analysis/signalp3.xml
243 tools/protein_analysis/suite_config.xml
244 tools/protein_analysis/tmhmm2.py
245 tools/protein_analysis/tmhmm2.xml
246 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
247 tools/protein_analysis/wolf_psort.py
248 tools/protein_analysis/wolf_psort.xml
194 249
195 This simplifies ensuring a consistent set of files is bundled each time, 250 This simplifies ensuring a consistent set of files is bundled each time,
196 including all the relevant test files. 251 including all the relevant test files.