Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison README.rst @ 27:b5e43dfe07ac draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
author pjbriggs
date Fri, 28 Sep 2018 11:28:17 -0400
parents bbfc9638ba84
children 18e6427c5e4a
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26:f0917c340f13 27:b5e43dfe07ac
27 at run time. 27 at run time.
28 28
29 1. Install the dependencies 29 1. Install the dependencies
30 --------------------------- 30 ---------------------------
31 31
32 The ``install_tool_deps.sh`` script can be used to fetch and install the 32 If the tool is installed from the Galaxy toolshed (recommended) then
33 dependencies locally, for example:: 33 the dependencies should be installed automatically and this step can
34 be skipped.
35
36 Otherwise the ``install_tool_deps.sh`` script can be used to fetch and
37 install the dependencies locally, for example::
34 38
35 install_tool_deps.sh /path/to/local_tool_dependencies 39 install_tool_deps.sh /path/to/local_tool_dependencies
36 40
37 This can take some time to complete. When finished it should have 41 This can take some time to complete. When finished it should have
38 created a set of directories containing the dependencies under the 42 created a set of directories containing the dependencies under the
39 specified top level directory. 43 specified top level directory.
44
45 *NB ``install_tool_deps.sh`` is no longer being maintained*
40 46
41 2. Install the tool files 47 2. Install the tool files
42 ------------------------- 48 -------------------------
43 49
44 The core tool is hosted on the Galaxy toolshed, so it can be installed 50 The core tool is hosted on the Galaxy toolshed, so it can be installed
201 - fasta-splitter 0.2.4 207 - fasta-splitter 0.2.4
202 - rdp_classifier 2.2 208 - rdp_classifier 2.2
203 209
204 The following dependencies are currently unavailable: 210 The following dependencies are currently unavailable:
205 211
206 - fasta_number (need 02jun2015) 212 - R 3.2.1 (installed from the toolshed as the bioconda version
213 has conflicts )
207 - microbiomeutil (need r20110519) 214 - microbiomeutil (need r20110519)
215
208 216
209 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be 217 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
210 handled outside of Galaxy's dependency management systems.) 218 handled outside of Galaxy's dependency management systems.)
211 219
212 History 220 History
213 ======= 221 =======
214 222
215 ========== ====================================================================== 223 ========== ======================================================================
216 Version Changes 224 Version Changes
217 ---------- ---------------------------------------------------------------------- 225 ---------- ----------------------------------------------------------------------
218 1.2.2.1 Update to get dependencies from bioconda 226 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
227 dependencies from bioconda and via tool_dependencies.xml
219 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes 228 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
220 jackknifed analysis which is not captured by Galaxy tool) 229 jackknifed analysis which is not captured by Galaxy tool)
221 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds 230 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
222 option to use the Human Oral Microbiome Database v15.1, and 231 option to use the Human Oral Microbiome Database v15.1, and
223 updates SILVA database to v123) 232 updates SILVA database to v123)