Mercurial > repos > peterjc > clinod

annotate tools/clinod/README.rst @ 4:4d9a4a43861b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
author peterjc
date Thu, 20 Nov 2014 06:15:49 -0500
parents 6a9debe4b860
children 9485cdfca57e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
1 Galaxy wrapper for Command line NoD predictor (v1.3)
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
2 ====================================================
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
6 See the licence text below.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
7
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
8 Command line NoD predictor is a tool for predicting nucleolar localization
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
9 sequences (NoLSs) in a FASTA file of proteins using a neural network. There
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
10 is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
11
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
12 This NoD wrapper is available from the Galaxy Tool Shed at:
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
13 http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
14
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
15
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
16 Automated Installation
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
17 ======================
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
18
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
19 This should be straightforward, Galaxy should automatically download and install
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
20 the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
21 Neural Network Simulator (SNNS), and set the ``$CLINOD`` to their folder.
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
22
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
23
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
24 Manual Installation
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
25 ===================
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
26 This wrapper expects the java binary to be on the system PATH, and to be able
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
27 to access command line NoD as ``$CLINOD/clinod-1.3.jar`` which means if you
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
28 used ``/opt/clinod/clinod-1.3.jar`` set the environment variable ``$CLINOD``
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
29 to ``/opt/clinod``
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
30
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
31 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
32 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
33 system path or located next to the JAR file, i.e. ``/opt/clinod/batchman``
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
34
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
35 To install the wrapper copy or move the following files under the Galaxy tools
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
36 folder, e.g. in a ``tools/clinod`` folder:
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
37
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
38 * ``clinod.xml`` (the Galaxy tool definition)
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
39 * ``README.rst`` (this file)
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
40
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
41 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
42 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
43 it next to them. Just add the line::
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
44
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
45 <tool file="clinod/clinod.xml" />
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
46
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
47 If you wish to run the unit tests, also move/copy the ``test-data/`` files
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
48 under Galaxy's ``test-data/`` folder. Then::
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
49
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
50 $ ./run_tests.sh -id clinod
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
51
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
52 That's it.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
53
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
54
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
55 History
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
56 =======
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
57
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
58 ======= ======================================================================
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
59 Version Changes
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
60 ------- ----------------------------------------------------------------------
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
61 v0.0.1 - Initial public release
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
62 v0.0.2 - Treat non-zero return codes as errors
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
63 v0.0.3 - Describe output table in help
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
64 v0.0.4 - Added unit test
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
65 v0.0.5 - Link to Tool Shed added to help text and this documentation.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
66 - Automated tool installation.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
67 v0.0.6 - Adopted standard MIT licence.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
68 - Use reStructuredText for this README file.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
69 - Updated citation information (Cock et al. 2013).
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
70 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
4
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
71 v0.0.7 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
4d9a4a43861b Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents: 3
diff changeset
72 - Tool definition now embeds citation information.
3
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
73 ======= ======================================================================
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
74
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
75
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
76 Developers
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
77 ==========
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
78
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
79 This script and related tools were initially developed on the following hg branch:
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
80 http://bitbucket.org/peterjc/galaxy-central/src/tools
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
81
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
82 Development has now moved to a dedicated GitHub repository:
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
83 https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
84
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
85 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
86 the following command from the Galaxy root folder::
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
87
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
88 $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
89
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
90 Check this worked::
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
91
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
92 $ tar -tzf clinod.tar.gz
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
93 tools/clinod/README.rst
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
94 tools/clinod/clinod.xml
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
95 tools/clinod/tool_dependencies.xml
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
96 test-data/four_human_proteins.fasta
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
97 test-data/four_human_proteins.clinod-1.3.tabular
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
98
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
99
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
100 Licence (MIT)
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
101 =============
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
102
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
103 Permission is hereby granted, free of charge, to any person obtaining a copy
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
104 of this software and associated documentation files (the "Software"), to deal
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
105 in the Software without restriction, including without limitation the rights
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
106 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
107 copies of the Software, and to permit persons to whom the Software is
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
108 furnished to do so, subject to the following conditions:
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
109
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
110 The above copyright notice and this permission notice shall be included in
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
111 all copies or substantial portions of the Software.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
112
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
113 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
114 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
115 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
116 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
117 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
118 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
119 THE SOFTWARE.
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
120
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
121 NOTE: This is the licence for the Galaxy Wrapper only. Command line
6a9debe4b860 Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
122 NoD is available and licenced separately.