Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate README.rst @ 29:31b7950136ed draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit afee03cb577aa68e650a2b7d65b31c000440d9ee
author pjbriggs
date Mon, 01 Oct 2018 07:31:44 -0400
parents b5e43dfe07ac
children 18e6427c5e4a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
1 Amplicon_analysis-galaxy
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
2 ========================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
4 A Galaxy tool wrapper to Mauro Tutino's ``Amplicon_analysis`` pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
5 script at https://github.com/MTutino/Amplicon_analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
6
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
7 The pipeline can analyse paired-end 16S rRNA data from Illumina Miseq
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
8 (Casava >= 1.8) and performs the following operations:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
9
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
10 * QC and clean up of input data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
11 * Removal of singletons and chimeras and building of OTU table
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
12 and phylogenetic tree
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
13 * Beta and alpha diversity of analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
14
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
15 Usage documentation
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
16 ===================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
17
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
18 Usage of the tool (including required inputs) is documented within
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
19 the ``help`` section of the tool XML.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
20
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
21 Installing the tool in a Galaxy instance
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
22 ========================================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
23
1
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
24 The following sections describe how to install the tool files,
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
25 dependencies and reference data, and how to configure the Galaxy
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
26 instance to detect the dependencies and reference data correctly
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
27 at run time.
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
28
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
29 1. Install the dependencies
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
30 ---------------------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
31
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
32 If the tool is installed from the Galaxy toolshed (recommended) then
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
33 the dependencies should be installed automatically and this step can
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
34 be skipped.
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
35
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
36 Otherwise the ``install_tool_deps.sh`` script can be used to fetch and
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
37 install the dependencies locally, for example::
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
38
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
39 install_tool_deps.sh /path/to/local_tool_dependencies
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
40
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
41 This can take some time to complete. When finished it should have
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
42 created a set of directories containing the dependencies under the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
43 specified top level directory.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
44
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
45 *NB ``install_tool_deps.sh`` is no longer being maintained*
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
46
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
47 2. Install the tool files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
48 -------------------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
49
1
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
50 The core tool is hosted on the Galaxy toolshed, so it can be installed
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
51 directly from there (this is the recommended route):
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
52
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
53 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
54
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
55 Alternatively it can be installed manually; in this case there are two
a00f366adc45 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents: 0
diff changeset
56 files to install:
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
57
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
58 * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
59 * ``amplicon_analysis_pipeline.py`` (the Python wrapper script)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
60
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
61 Put these in a directory that is visible to Galaxy (e.g. a
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
62 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
63 file to tell Galaxy to offer the tool by adding the line e.g.::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
64
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
65 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
66
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
67 3. Install the reference data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
68 -----------------------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
69
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
70 The script ``References.sh`` from the pipeline package at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
71 https://github.com/MTutino/Amplicon_analysis can be run to install
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
72 the reference data, for example::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
73
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
74 cd /path/to/pipeline/data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
75 wget https://github.com/MTutino/Amplicon_analysis/raw/master/References.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
76 /bin/bash ./References.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
77
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
78 will install the data in ``/path/to/pipeline/data``.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
79
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
80 **NB** The final amount of data downloaded and uncompressed will be
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
81 around 6GB.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
82
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
83 4. Configure dependencies and reference data in Galaxy
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
84 ------------------------------------------------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
85
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
86 The final steps are to make your Galaxy installation aware of the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
87 tool dependencies and reference data, so it can locate them both when
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
88 the tool is run.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
89
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
90 To target the tool dependencies installed previously, add the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
91 following lines to the ``dependency_resolvers_conf.xml`` file in the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
92 Galaxy ``config`` directory::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
93
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
94 <dependency_resolvers>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
95 ...
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
96 <galaxy_packages base_path="/path/to/local_tool_dependencies" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
97 <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
98 ...
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
99 </dependency_resolvers>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
100
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
101 (NB it is recommended to place these *before* the ``<conda ... />``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
102 resolvers)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
103
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
104 (If you're not familiar with dependency resolvers in Galaxy then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
105 see the documentation at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
106 https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
107 for more details.)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
108
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
109 The tool locates the reference data via an environment variable called
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
110 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
111 directory where the reference data has been installed.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
112
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
113 There are various ways to do this, depending on how your Galaxy
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
114 installation is configured:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
115
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
116 * **For local instances:** add a line to set it in the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
117 ``config/local_env.sh`` file of your Galaxy installation, e.g.::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
118
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
119 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
120
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
121 * **For production instances:** set the value in the ``job_conf.xml``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
122 configuration file, e.g.::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
123
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
124 <destination id="amplicon_analysis">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
125 <env id="AMPLICON_ANALYSIS_REF_DATA_PATH">/path/to/pipeline/data</env>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
126 </destination>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
127
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
128 and then specify that the pipeline tool uses this destination::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
129
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
130 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
131
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
132 (For more about job destinations see the Galaxy documentation at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
133 https://galaxyproject.org/admin/config/jobs/#job-destinations)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
134
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
135 5. Enable rendering of HTML outputs from pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
136 -------------------------------------------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
137
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
138 To ensure that HTML outputs are displayed correctly in Galaxy
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
139 (for example the Vsearch OTU table heatmaps), Galaxy needs to be
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
140 configured not to sanitize the outputs from the ``Amplicon_analysis``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
141 tool.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
142
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
143 Either:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
144
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
145 * **For local instances:** set ``sanitize_all_html = False`` in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
146 ``config/galaxy.ini`` (nb don't do this on production servers or
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
147 public instances!); or
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
148
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
149 * **For production instances:** add the ``Amplicon_analysis`` tool
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
150 to the display whitelist in the Galaxy instance:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
151
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
152 - Set ``sanitize_whitelist_file = config/whitelist.txt`` in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
153 ``config/galaxy.ini`` and restart Galaxy;
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
154 - Go to ``Admin>Manage Display Whitelist``, check the box for
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
155 ``Amplicon_analysis`` (hint: use your browser's 'find-in-page'
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
156 search function to help locate it) and click on
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
157 ``Submit new whitelist`` to update the settings.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
158
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
159 Additional details
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
160 ==================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
161
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
162 Some other things to be aware of:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
163
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
164 * Note that using the Silva database requires a minimum of 18Gb RAM
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
165
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
166 Known problems
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
167 ==============
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
168
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
169 * Only the ``VSEARCH`` pipeline in Mauro's script is currently
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
170 available via the Galaxy tool; the ``USEARCH`` and ``QIIME``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
171 pipelines have yet to be implemented.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
172 * The images in the tool help section are not visible if the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
173 tool has been installed locally, or if it has been installed in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
174 a Galaxy instance which is served from a subdirectory.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
175
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
176 These are both problems with Galaxy and not the tool, see
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
177 https://github.com/galaxyproject/galaxy/issues/4490 and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
178 https://github.com/galaxyproject/galaxy/issues/1676
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
179
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
180 Appendix: availability of tool dependencies
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
181 ===========================================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
182
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
183 The tool takes its dependencies from the underlying pipeline script (see
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
184 https://github.com/MTutino/Amplicon_analysis/blob/master/README.md
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
185 for details).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
186
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
187 As noted above, currently the ``install_tool_deps.sh`` script can be
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
188 used to manually install the dependencies for a local tool install.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
189
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
190 In principle these should also be available if the tool were installed
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
191 from a toolshed. However it would be preferrable in this case to get as
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
192 many of the dependencies as possible via the ``conda`` dependency
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
193 resolver.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
194
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
195 The following are known to be available via conda, with the required
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
196 version:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
197
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
198 - cutadapt 1.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
199 - sickle-trim 1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
200 - bioawk 1.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
201 - fastqc 0.11.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
202 - R 3.2.0
5
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
203 - spades 3.5.0
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
204 - qiime 1.8.0
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
205 - blast-legacy 2.2.26
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
206 - vsearch 1.1.3
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
207 - fasta-splitter 0.2.4
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
208 - rdp_classifier 2.2
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
209
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
210 The following dependencies are currently unavailable:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
211
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
212 - R 3.2.1 (installed from the toolshed as the bioconda version
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
213 has conflicts )
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
214 - microbiomeutil (need r20110519)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
215
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
216
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
217 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
218 handled outside of Galaxy's dependency management systems.)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
219
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
220 History
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
221 =======
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
222
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
223 ========== ======================================================================
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
224 Version Changes
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
225 ---------- ----------------------------------------------------------------------
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
226 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 5
diff changeset
227 dependencies from bioconda and via tool_dependencies.xml
4
013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2.
pjbriggs
parents: 2
diff changeset
228 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2.
pjbriggs
parents: 2
diff changeset
229 jackknifed analysis which is not captured by Galaxy tool)
2
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 1
diff changeset
230 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 1
diff changeset
231 option to use the Human Oral Microbiome Database v15.1, and
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 1
diff changeset
232 updates SILVA database to v123)
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
233 1.1.0 First official version on Galaxy toolshed.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
234 1.0.6 Expand inline documentation to provide detailed usage guidance.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
235 1.0.5 Updates including:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
236
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
237 - Capture read counts from quality control as new output dataset
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
238 - Capture FastQC per-base quality boxplots for each sample as
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
239 new output dataset
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
240 - Add support for -l option (sliding window length for trimming)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
241 - Default for -L set to "200"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
242 1.0.4 Various updates:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
243
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
244 - Additional outputs are captured when a "Categories" file is
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
245 supplied (alpha diversity rarefaction curves and boxplots)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
246 - Sample names derived from Fastqs in a collection of pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
247 are trimmed to SAMPLE_S* (for Illumina-style Fastq filenames)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
248 - Input Fastqs can now be of more general ``fastq`` type
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
249 - Log file outputs are captured in new output dataset
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
250 - User can specify a "title" for the job which is copied into
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
251 the dataset names (to distinguish outputs from different runs)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
252 - Improved detection and reporting of problems with input
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
253 Metatable
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
254 1.0.3 Take the sample names from the collection dataset names when
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
255 using collection as input (this is now the default input mode);
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
256 collect additional output dataset; disable ``usearch``-based
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
257 pipelines (i.e. ``UPARSE`` and ``QIIME``).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
258 1.0.2 Enable support for FASTQs supplied via dataset collections and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
259 fix some broken output datasets.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
260 1.0.1 Initial version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
261 ========== ======================================================================