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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit c3970ae16b02774148dbf950880f07255734a9a8-dirty
author pjbriggs
date Wed, 17 Oct 2018 08:14:27 -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 If the tool is installed from the Galaxy toolshed (recommended) then
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::
38
39 install_tool_deps.sh /path/to/local_tool_dependencies
40
41 This can take some time to complete. When finished it should have
42 created a set of directories containing the dependencies under the
43 specified top level directory.
44
45 *NB ``install_tool_deps.sh`` is no longer being maintained*
46
47 2. Install the tool files
48 -------------------------
49 31
50 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
51 directly from there (this is the recommended route): 33 directly from there (this is the recommended route):
52 34
53 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/ 35 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
62 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml`` 44 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
63 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.::
64 46
65 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" /> 47 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
66 48
67 3. Install the reference data 49 2. Install the reference data
68 ----------------------------- 50 -----------------------------
69 51
70 The script ``References.sh`` from the pipeline package at 52 The script ``References.sh`` from the pipeline package at
71 https://github.com/MTutino/Amplicon_analysis can be run to install 53 https://github.com/MTutino/Amplicon_analysis can be run to install
72 the reference data, for example:: 54 the reference data, for example::
76 /bin/bash ./References.sh 58 /bin/bash ./References.sh
77 59
78 will install the data in ``/path/to/pipeline/data``. 60 will install the data in ``/path/to/pipeline/data``.
79 61
80 **NB** The final amount of data downloaded and uncompressed will be 62 **NB** The final amount of data downloaded and uncompressed will be
81 around 6GB. 63 around 9GB.
82 64
83 4. Configure dependencies and reference data in Galaxy 65 3. Configure reference data location in Galaxy
84 ------------------------------------------------------ 66 ----------------------------------------------
85 67
86 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
87 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
88 the tool is run. 70 tool is run.
89
90 To target the tool dependencies installed previously, add the
91 following lines to the ``dependency_resolvers_conf.xml`` file in the
92 Galaxy ``config`` directory::
93
94 <dependency_resolvers>
95 ...
96 <galaxy_packages base_path="/path/to/local_tool_dependencies" />
97 <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
98 ...
99 </dependency_resolvers>
100
101 (NB it is recommended to place these *before* the ``<conda ... />``
102 resolvers)
103
104 (If you're not familiar with dependency resolvers in Galaxy then
105 see the documentation at
106 https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
107 for more details.)
108 71
109 The tool locates the reference data via an environment variable called 72 The tool locates the reference data via an environment variable called
110 ``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
111 directory where the reference data has been installed. 74 directory where the reference data has been installed.
112 75
113 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
114 installation is configured: 77 installation is configured:
115 78
116 * **For local instances:** add a line to set it in the 79 * **For local instances:** add a line to set it in the
117 ``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.::
118 82
119 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data 83 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
120 84
121 * **For production instances:** set the value in the ``job_conf.xml`` 85 * **For production instances:** set the value in the ``job_conf.xml``
122 configuration file, e.g.:: 86 configuration file, e.g.::
128 and then specify that the pipeline tool uses this destination:: 92 and then specify that the pipeline tool uses this destination::
129 93
130 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/> 94 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
131 95
132 (For more about job destinations see the Galaxy documentation at 96 (For more about job destinations see the Galaxy documentation at
133 https://galaxyproject.org/admin/config/jobs/#job-destinations) 97 https://docs.galaxyproject.org/en/master/admin/jobs.html#job-destinations)
134 98
135 5. Enable rendering of HTML outputs from pipeline 99 4. Enable rendering of HTML outputs from pipeline
136 ------------------------------------------------- 100 -------------------------------------------------
137 101
138 To ensure that HTML outputs are displayed correctly in Galaxy 102 To ensure that HTML outputs are displayed correctly in Galaxy
139 (for example the Vsearch OTU table heatmaps), Galaxy needs to be 103 (for example the Vsearch OTU table heatmaps), Galaxy needs to be
140 configured not to sanitize the outputs from the ``Amplicon_analysis`` 104 configured not to sanitize the outputs from the ``Amplicon_analysis``
175 139
176 These are both problems with Galaxy and not the tool, see 140 These are both problems with Galaxy and not the tool, see
177 https://github.com/galaxyproject/galaxy/issues/4490 and 141 https://github.com/galaxyproject/galaxy/issues/4490 and
178 https://github.com/galaxyproject/galaxy/issues/1676 142 https://github.com/galaxyproject/galaxy/issues/1676
179 143
144 Appendix: installing the dependencies manually
145 ==============================================
146
147 If the tool is installed from the Galaxy toolshed (recommended) then
148 the dependencies should be installed automatically and this step can
149 be skipped.
150
151 Otherwise the ``install_amplicon_analysis_deps.sh`` script can be used
152 to fetch and install the dependencies locally, for example::
153
154 install_amplicon_analysis.sh /path/to/local_tool_dependencies
155
156 (This is the same script as is used to install dependencies from the
157 toolshed.) This can take some time to complete, and when completed will
158 have created a directory called ``Amplicon_analysis-1.2.3`` containing
159 the dependencies under the specified top level directory.
160
161 **NB** The installed dependencies will occupy around 2.6G of disk
162 space.
163
164 You will need to make sure that the ``bin`` subdirectory of this
165 directory is on Galaxy's ``PATH`` at runtime, for the tool to be able
166 to access the dependencies - for example by adding a line to the
167 ``local_env.sh`` file like::
168
169 export PATH=/path/to/local_tool_dependencies/Amplicon_analysis-1.2.3/bin:$PATH
170
180 History 171 History
181 ======= 172 =======
182 173
183 ========== ====================================================================== 174 ========== ======================================================================
184 Version Changes 175 Version Changes
185 ---------- ---------------------------------------------------------------------- 176 ---------- ----------------------------------------------------------------------
186 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install 177 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
187 dependencies from bioconda and via tool_dependencies.xml. 178 dependencies via tool_dependencies.xml.
188 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
189 jackknifed analysis which is not captured by Galaxy tool) 180 jackknifed analysis which is not captured by Galaxy tool)
190 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
191 option to use the Human Oral Microbiome Database v15.1, and 182 option to use the Human Oral Microbiome Database v15.1, and
192 updates SILVA database to v123) 183 updates SILVA database to v123)