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comparison README.rst @ 1:a00f366adc45 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
author pjbriggs
date Thu, 09 Nov 2017 10:09:33 -0500
parents b433086738d6
children a898ee628343
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19 the ``help`` section of the tool XML. 19 the ``help`` section of the tool XML.
20 20
21 Installing the tool in a Galaxy instance 21 Installing the tool in a Galaxy instance
22 ======================================== 22 ========================================
23 23
24 The tool is not currently hosted on a Galaxy toolshed both the tool 24 The following sections describe how to install the tool files,
25 files and the dependencies must be installed manually. In addition 25 dependencies and reference data, and how to configure the Galaxy
26 it is necessary to fetch and install the reference data. 26 instance to detect the dependencies and reference data correctly
27 at run time.
27 28
28 1. Install the dependencies 29 1. Install the dependencies
29 --------------------------- 30 ---------------------------
30 31
31 The ``install_tool_deps.sh`` script can be used to fetch and install the 32 The ``install_tool_deps.sh`` script can be used to fetch and install the
38 specified top level directory. 39 specified top level directory.
39 40
40 2. Install the tool files 41 2. Install the tool files
41 ------------------------- 42 -------------------------
42 43
43 There are two files to install: 44 The core tool is hosted on the Galaxy toolshed, so it can be installed
45 directly from there (this is the recommended route):
46
47 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
48
49 Alternatively it can be installed manually; in this case there are two
50 files to install:
44 51
45 * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition) 52 * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition)
46 * ``amplicon_analysis_pipeline.py`` (the Python wrapper script) 53 * ``amplicon_analysis_pipeline.py`` (the Python wrapper script)
47 54
48 Put these in a directory that is visible to Galaxy (e.g. a 55 Put these in a directory that is visible to Galaxy (e.g. a