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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 15390f18b91d838880d952eb2714f689bbd8a042
author pjbriggs
date Thu, 18 Oct 2018 09:18:04 -0400
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24 The following sections describe how to install the tool files, 24 The following sections describe how to install the tool files,
25 dependencies and reference data, and how to configure the Galaxy 25 dependencies and reference data, and how to configure the Galaxy
26 instance to detect the dependencies and reference data correctly 26 instance to detect the dependencies and reference data correctly
27 at run time. 27 at run time.
28 28
29 1. Install the dependencies 29 1. Install the tool from the toolshed
30 --------------------------- 30 -------------------------------------
31
32 The ``install_tool_deps.sh`` script can be used to fetch and install the
33 dependencies locally, for example::
34
35 install_tool_deps.sh /path/to/local_tool_dependencies
36
37 This can take some time to complete. When finished it should have
38 created a set of directories containing the dependencies under the
39 specified top level directory.
40
41 2. Install the tool files
42 -------------------------
43 31
44 The core tool is hosted on the Galaxy toolshed, so it can be installed 32 The core tool is hosted on the Galaxy toolshed, so it can be installed
45 directly from there (this is the recommended route): 33 directly from there (this is the recommended route):
46 34
47 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/ 35 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
56 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml`` 44 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
57 file to tell Galaxy to offer the tool by adding the line e.g.:: 45 file to tell Galaxy to offer the tool by adding the line e.g.::
58 46
59 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" /> 47 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
60 48
61 3. Install the reference data 49 2. Install the reference data
62 ----------------------------- 50 -----------------------------
63 51
64 The script ``References.sh`` from the pipeline package at 52 The script ``References.sh`` from the pipeline package at
65 https://github.com/MTutino/Amplicon_analysis can be run to install 53 https://github.com/MTutino/Amplicon_analysis can be run to install
66 the reference data, for example:: 54 the reference data, for example::
70 /bin/bash ./References.sh 58 /bin/bash ./References.sh
71 59
72 will install the data in ``/path/to/pipeline/data``. 60 will install the data in ``/path/to/pipeline/data``.
73 61
74 **NB** The final amount of data downloaded and uncompressed will be 62 **NB** The final amount of data downloaded and uncompressed will be
75 around 6GB. 63 around 9GB.
76 64
77 4. Configure dependencies and reference data in Galaxy 65 3. Configure reference data location in Galaxy
78 ------------------------------------------------------ 66 ----------------------------------------------
79 67
80 The final steps are to make your Galaxy installation aware of the 68 The final step is to make your Galaxy installation aware of the
81 tool dependencies and reference data, so it can locate them both when 69 location of the reference data, so it can locate them both when the
82 the tool is run. 70 tool is run.
83
84 To target the tool dependencies installed previously, add the
85 following lines to the ``dependency_resolvers_conf.xml`` file in the
86 Galaxy ``config`` directory::
87
88 <dependency_resolvers>
89 ...
90 <galaxy_packages base_path="/path/to/local_tool_dependencies" />
91 <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
92 ...
93 </dependency_resolvers>
94
95 (NB it is recommended to place these *before* the ``<conda ... />``
96 resolvers)
97
98 (If you're not familiar with dependency resolvers in Galaxy then
99 see the documentation at
100 https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
101 for more details.)
102 71
103 The tool locates the reference data via an environment variable called 72 The tool locates the reference data via an environment variable called
104 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent 73 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
105 directory where the reference data has been installed. 74 directory where the reference data has been installed.
106 75
107 There are various ways to do this, depending on how your Galaxy 76 There are various ways to do this, depending on how your Galaxy
108 installation is configured: 77 installation is configured:
109 78
110 * **For local instances:** add a line to set it in the 79 * **For local instances:** add a line to set it in the
111 ``config/local_env.sh`` file of your Galaxy installation, e.g.:: 80 ``config/local_env.sh`` file of your Galaxy installation (you
81 may need to create a new empty file first), e.g.::
112 82
113 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data 83 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
114 84
115 * **For production instances:** set the value in the ``job_conf.xml`` 85 * **For production instances:** set the value in the ``job_conf.xml``
116 configuration file, e.g.:: 86 configuration file, e.g.::
122 and then specify that the pipeline tool uses this destination:: 92 and then specify that the pipeline tool uses this destination::
123 93
124 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/> 94 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
125 95
126 (For more about job destinations see the Galaxy documentation at 96 (For more about job destinations see the Galaxy documentation at
127 https://galaxyproject.org/admin/config/jobs/#job-destinations) 97 https://docs.galaxyproject.org/en/master/admin/jobs.html#job-destinations)
128 98
129 5. Enable rendering of HTML outputs from pipeline 99 4. Enable rendering of HTML outputs from pipeline
130 ------------------------------------------------- 100 -------------------------------------------------
131 101
132 To ensure that HTML outputs are displayed correctly in Galaxy 102 To ensure that HTML outputs are displayed correctly in Galaxy
133 (for example the Vsearch OTU table heatmaps), Galaxy needs to be 103 (for example the Vsearch OTU table heatmaps), Galaxy needs to be
134 configured not to sanitize the outputs from the ``Amplicon_analysis`` 104 configured not to sanitize the outputs from the ``Amplicon_analysis``
169 139
170 These are both problems with Galaxy and not the tool, see 140 These are both problems with Galaxy and not the tool, see
171 https://github.com/galaxyproject/galaxy/issues/4490 and 141 https://github.com/galaxyproject/galaxy/issues/4490 and
172 https://github.com/galaxyproject/galaxy/issues/1676 142 https://github.com/galaxyproject/galaxy/issues/1676
173 143
174 Appendix: availability of tool dependencies 144 Appendix: installing the dependencies manually
175 =========================================== 145 ==============================================
176 146
177 The tool takes its dependencies from the underlying pipeline script (see 147 If the tool is installed from the Galaxy toolshed (recommended) then
178 https://github.com/MTutino/Amplicon_analysis/blob/master/README.md 148 the dependencies should be installed automatically and this step can
179 for details). 149 be skipped.
180 150
181 As noted above, currently the ``install_tool_deps.sh`` script can be 151 Otherwise the ``install_amplicon_analysis_deps.sh`` script can be used
182 used to manually install the dependencies for a local tool install. 152 to fetch and install the dependencies locally, for example::
183 153
184 In principle these should also be available if the tool were installed 154 install_amplicon_analysis.sh /path/to/local_tool_dependencies
185 from a toolshed. However it would be preferrable in this case to get as 155
186 many of the dependencies as possible via the ``conda`` dependency 156 (This is the same script as is used to install dependencies from the
187 resolver. 157 toolshed.) This can take some time to complete, and when completed will
188 158 have created a directory called ``Amplicon_analysis-1.2.3`` containing
189 The following are known to be available via conda, with the required 159 the dependencies under the specified top level directory.
190 version: 160
191 161 **NB** The installed dependencies will occupy around 2.6G of disk
192 - cutadapt 1.8.1 162 space.
193 - sickle-trim 1.33 163
194 - bioawk 1.0 164 You will need to make sure that the ``bin`` subdirectory of this
195 - fastqc 0.11.3 165 directory is on Galaxy's ``PATH`` at runtime, for the tool to be able
196 - R 3.2.0 166 to access the dependencies - for example by adding a line to the
197 167 ``local_env.sh`` file like::
198 Some dependencies are available but with the "wrong" versions: 168
199 169 export PATH=/path/to/local_tool_dependencies/Amplicon_analysis-1.2.3/bin:$PATH
200 - spades (need 3.5.0)
201 - qiime (need 1.8.0)
202 - blast (need 2.2.26)
203 - vsearch (need 1.1.3)
204
205 The following dependencies are currently unavailable:
206
207 - fasta_number (need 02jun2015)
208 - fasta-splitter (need 0.2.4)
209 - rdp_classifier (need 2.2)
210 - microbiomeutil (need r20110519)
211
212 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
213 handled outside of Galaxy's dependency management systems.)
214 170
215 History 171 History
216 ======= 172 =======
217 173
218 ========== ====================================================================== 174 ========== ======================================================================
219 Version Changes 175 Version Changes
220 ---------- ---------------------------------------------------------------------- 176 ---------- ----------------------------------------------------------------------
177 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
178 dependencies via tool_dependencies.xml.
221 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes 179 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
222 jackknifed analysis which is not captured by Galaxy tool) 180 jackknifed analysis which is not captured by Galaxy tool)
223 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds 181 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
224 option to use the Human Oral Microbiome Database v15.1, and 182 option to use the Human Oral Microbiome Database v15.1, and
225 updates SILVA database to v123) 183 updates SILVA database to v123)