Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa
author pjbriggs
date Tue, 02 Oct 2018 08:58:13 -0400
parents b5e43dfe07ac
children d19fca1c009c
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176 These are both problems with Galaxy and not the tool, see 176 These are both problems with Galaxy and not the tool, see
177 https://github.com/galaxyproject/galaxy/issues/4490 and 177 https://github.com/galaxyproject/galaxy/issues/4490 and
178 https://github.com/galaxyproject/galaxy/issues/1676 178 https://github.com/galaxyproject/galaxy/issues/1676
179 179
180 Appendix: availability of tool dependencies
181 ===========================================
182
183 The tool takes its dependencies from the underlying pipeline script (see
184 https://github.com/MTutino/Amplicon_analysis/blob/master/README.md
185 for details).
186
187 As noted above, currently the ``install_tool_deps.sh`` script can be
188 used to manually install the dependencies for a local tool install.
189
190 In principle these should also be available if the tool were installed
191 from a toolshed. However it would be preferrable in this case to get as
192 many of the dependencies as possible via the ``conda`` dependency
193 resolver.
194
195 The following are known to be available via conda, with the required
196 version:
197
198 - cutadapt 1.8.1
199 - sickle-trim 1.33
200 - bioawk 1.0
201 - fastqc 0.11.3
202 - R 3.2.0
203 - spades 3.5.0
204 - qiime 1.8.0
205 - blast-legacy 2.2.26
206 - vsearch 1.1.3
207 - fasta-splitter 0.2.4
208 - rdp_classifier 2.2
209
210 The following dependencies are currently unavailable:
211
212 - R 3.2.1 (installed from the toolshed as the bioconda version
213 has conflicts )
214 - microbiomeutil (need r20110519)
215
216
217 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
218 handled outside of Galaxy's dependency management systems.)
219
220 History 180 History
221 ======= 181 =======
222 182
223 ========== ====================================================================== 183 ========== ======================================================================
224 Version Changes 184 Version Changes
225 ---------- ---------------------------------------------------------------------- 185 ---------- ----------------------------------------------------------------------
226 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install 186 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
227 dependencies from bioconda and via tool_dependencies.xml 187 dependencies from bioconda and via tool_dependencies.xml.
228 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes 188 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
229 jackknifed analysis which is not captured by Galaxy tool) 189 jackknifed analysis which is not captured by Galaxy tool)
230 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds 190 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
231 option to use the Human Oral Microbiome Database v15.1, and 191 option to use the Human Oral Microbiome Database v15.1, and
232 updates SILVA database to v123) 192 updates SILVA database to v123)