Mercurial > repos > peterjc > effectivet3

annotate tools/effectiveT3/README.rst @ 9:512530020360 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.18 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:17:17 -0400
parents 60a9b3f760cc
children a46d7861c32c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
1 Galaxy wrapper for EffectiveT3 v1.0.1
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
2 =====================================
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
3
8
60a9b3f760cc v0.0.17 Used cached URL, python style updates
peterjc
parents: 7
diff changeset
4 This wrapper is copyright 2011-2017 by Peter Cock, The James Hutton Institute
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
6 See the licence text below.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
7
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
9
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
10 Jehl, Arnold and Rattei.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
11 Effective - a database of predicted secreted bacterial proteins
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
12 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
13 http://dx.doi.org/10.1093/nar/gkq1154
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
14
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
15 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
16 Sequence-based prediction of type III secreted proteins.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
17 PLoS Pathog. 5(4):e1000376, 2009.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
18 http://dx.doi.org/10.1371/journal.ppat.1000376
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
19
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
20 http://effectors.org/
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
21
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
22 This wrapper is available from the Galaxy Tool Shed at:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
23 http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
24
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
25
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
26 Automated Installation
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
27 ======================
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
28
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
29 This should be straightforward, Galaxy should automatically download and install
7
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
30 the Jar files for effectiveT3 v1.0.1 and its associated models (animal, plant and
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
31 standard).
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
32
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
33
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
34 Manual Installation
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
35 ===================
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
36
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
37 You can change the path by setting the environment variable ``$EFFECTIVET3`` to the
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
38 relevant folder, but by default it expects the following files to be installed
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
39 at these locations::
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
40
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
41 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
42 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
43 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
44 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
45
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
46 To install the wrapper copy or move the following files under the Galaxy tools
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
47 folder, e.g. in a tools/effectiveT3 folder:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
48
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
49 * ``effectiveT3.xml`` (the Galaxy tool definition)
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
50 * ``effectiveT3.py`` (the Python wrapper script)
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
51 * ``README.rst`` (this file)
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
52
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
53 Also copy ``effectiveT3.loc.sample`` to ``effectiveT3.loc`` in the ``tool-data``
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
54 folder (and edit if appropriate, e.g. to add or remove a model).
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
55
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
56 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
57 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
58 it next to them. Just add the line::
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
59
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
60 <tool file="effectiveT3/effectiveT3.xml" />
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
61
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
62 If you wish to run the unit tests, also move/copy the ``test-data/`` files
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
63 under Galaxy's ``test-data/`` folder. Then::
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
64
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
65 $ ./run_tests.sh -id effectiveT3
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
66
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
67 That's it.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
68
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
69
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
70 History
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
71 =======
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
72
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
73 ======= ======================================================================
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
74 Version Changes
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
75 ------- ----------------------------------------------------------------------
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
76 v0.0.7 - Initial public release
7
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
77 v0.0.8 - Include ``effectiveT3.loc.sample`` in Tool Shed
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
78 v0.0.9 - Check the return code for errors in the XML
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
79 v0.0.10 - Added unit test
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
80 v0.0.11 - Automated installation
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
81 - Record version of Python script when called from Galaxy
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
82 - Link to Tool Shed added to help text and this documentation.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
83 v0.0.12 - More explicit naming of the output dataset.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
84 - Adopt standard MIT licence.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
85 - Use reStructuredText for this README file.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
86 - Updated citation information (Cock et al. 2013).
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
87 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
88 v0.0.13 - Relax unit test to allow for small floating point score difference.
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
89 - Tool definition now embeds citation information.
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
90 v0.0.14 - Fixed error handling in ``effectiveT3.py``.
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
91 v0.0.15 - Reorder XML elements (internal change only).
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
92 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
7
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
93 v0.0.16 - Updated URLs to download the tool and models.
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
94 - Includes new standard classification model v2.0.2 (Sep 2015)
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
95 as the default entry in ``tool-data/effectiveT3.loc``
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
96 - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar``
8
60a9b3f760cc v0.0.17 Used cached URL, python style updates
peterjc
parents: 7
diff changeset
97 v0.0.17 - Update tool dependency definition to use cached URL.
60a9b3f760cc v0.0.17 Used cached URL, python style updates
peterjc
parents: 7
diff changeset
98 - Minor internal changes to Python script for error reporting & style.
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
99 v0.0.18 - Use ``<command detect_errors="aggressive">`` (internal change only).
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
100 - Single quote command line arguments (internal change only).
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
101 ======= ======================================================================
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
102
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
103
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
104 Developers
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
105 ==========
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
106
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
107 This script and related tools were initially developed on the following hg branch:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
108 http://bitbucket.org/peterjc/galaxy-central/src/tools
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
109
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
110 Development has now moved to a dedicated GitHub repository:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
111 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
112
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
113 For pushing a release to the test or main "Galaxy Tool Shed", use the following
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
114 Planemo commands (which requires you have set your Tool Shed access details in
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
115 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
116
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
117 $ planemo shed_update -t testtoolshed --check_diff tools/effectiveT3/
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
118 ...
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
119
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
120 or::
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
121
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
122 $ planemo shed_update -t toolshed --check_diff tools/effectiveT3/
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
123 ...
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
124
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
125 To just build and check the tar ball, use::
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
126
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
127 $ planemo shed_upload --tar_only tools/effectiveT3/
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
128 ...
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
129 $ tar -tzf shed_upload.tar.gz
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
130 tool-data/effectiveT3.loc.sample
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
131 test-data/empty.fasta
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
132 test-data/empty_effectiveT3.tabular
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
133 test-data/four_human_proteins.fasta
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
134 test-data/four_human_proteins.effectiveT3.tabular
6
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
135 tool-data/effectiveT3.loc.sample
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
136 tools/effectiveT3/README.rst
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
137 tools/effectiveT3/effectiveT3.py
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
138 tools/effectiveT3/effectiveT3.xml
0f6eb4a75000 v0.0.15 internal changes; v0.0.14 fixed error handling
peterjc
parents: 5
diff changeset
139 tools/effectiveT3/tool_dependencies.xml
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
140
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
141
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
142 Licence (MIT)
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
143 =============
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
144
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
145 Permission is hereby granted, free of charge, to any person obtaining a copy
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
146 of this software and associated documentation files (the "Software"), to deal
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
147 in the Software without restriction, including without limitation the rights
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
148 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
149 copies of the Software, and to permit persons to whom the Software is
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
150 furnished to do so, subject to the following conditions:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
151
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
152 The above copyright notice and this permission notice shall be included in
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
153 all copies or substantial portions of the Software.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
154
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
155 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
156 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
157 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
158 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
159 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
160 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
161 THE SOFTWARE.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
162
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
163 NOTE: This is the licence for the Galaxy Wrapper only.
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
164 EffectiveT3 is available and licenced separately.