Mercurial > repos > peterjc > nlstradamus

comparison tools/nlstradamus/README.rst @ 4:1458e60f3fd0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.10 internal changes; v0.0.9 citation
author peterjc
date Wed, 05 Aug 2015 12:23:05 -0400
parents b2e648e55ed7
children e8f15b0136cd
comparison
equal deleted inserted replaced
3:b2e648e55ed7 4:1458e60f3fd0
1 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version) 1 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
2 ========================================================= 2 =========================================================
3 3
4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence). 6 See the licence text below (MIT licence).
7 7
8 NLStradamus is a command line tool for predicting nuclear localization 8 NLStradamus is a command line tool for predicting nuclear localization
9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM). 9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
33 the C++ implementation of NLStradamus v1.8, and run the unit tests. 33 the C++ implementation of NLStradamus v1.8, and run the unit tests.
34 34
35 35
36 Manual Installation 36 Manual Installation
37 =================== 37 ===================
38 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system 38 This wrapper expects the compiled C++ binary "NLStradamus" to be on the ``$PATH``.
39 PATH.
40 39
41 To install the wrapper copy or move the following files under the Galaxy tools 40 To install the wrapper copy or move the following files under the Galaxy tools
42 folder, e.g. in a tools/protein_analysis folder: 41 folder, e.g. in a tools/protein_analysis folder:
43 42
44 * nlstradamus.xml (the Galaxy tool definition) 43 * ``nlstradamus.xml`` (the Galaxy tool definition)
45 * nlstradamus.txt (this README file) 44 * ``nlstradamus.txt`` (this README file)
46 45
47 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the 46 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
48 tool. If you are using other protein analysis tools like TMHMM or SignalP, put 47 the tool. If you are using other protein analysis tools like TMHMM or SignalP,
49 it next to them. Just add the line (matching the chosen install path):: 48 put it next to them. Just add the line (matching the chosen install path)::
50 49
51 <tool file="protein_analysis/nlstradamus.xml" /> 50 <tool file="protein_analysis/nlstradamus.xml" />
52 51
53 If you wish to run the unit tests, also add this to tools_conf.xml.sample 52 If you wish to run the unit tests, also move/copy the ``test-data/`` files
54 and move/copy the test-data files under Galaxy's test-data folder. Then:: 53 under Galaxy's ``test-data/`` folder. Then::
55 54
56 $ ./run_functional_tests.sh -id nlstradamus 55 $ ./run_tests.sh -id nlstradamus
57 56
58 That's it. 57 That's it.
59 58
60 59
61 History 60 History
75 v0.0.8 - Link to Tool Shed added to help text and this documentation. 74 v0.0.8 - Link to Tool Shed added to help text and this documentation.
76 - Use reStructuredText for this README file. 75 - Use reStructuredText for this README file.
77 - Adopted standard MIT licence. 76 - Adopted standard MIT licence.
78 - Updated citation information (Cock et al. 2013). 77 - Updated citation information (Cock et al. 2013).
79 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 78 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
79 v0.0.9 - Tool definition now embeds citation information.
80 v0.0.10 - Reorder XML elements (internal change only).
81 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
80 ======= ====================================================================== 82 ======= ======================================================================
81 83
82 84
83 Developers 85 Developers
84 ========== 86 ==========
85 87
86 This script and related tools are being developed on the following hg branch: 88 This script and related tools were initially developed on the following hg branch:
87 http://bitbucket.org/peterjc/galaxy-central/src/tools 89 http://bitbucket.org/peterjc/galaxy-central/src/tools
88 90
89 Development has now moved to a dedicated GitHub repository: 91 Development has now moved to a dedicated GitHub repository:
90 https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 92 https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
91 93
92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
93 the following command from the Galaxy root folder::
94 94
95 $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular 95 For pushing a release to the test or main "Galaxy Tool Shed", use the following
96 Planemo commands (which requires you have set your Tool Shed access details in
97 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
96 98
97 Check this worked:: 99 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/nlstradamus/
100 ...
98 101
99 $ tar -tzf nlstradmus.tar.gz 102 or::
103
104 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/nlstradamus/
105 ...
106
107 To just build and check the tar ball, use::
108
109 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/nlstradamus/
110 ...
111 $ tar -tzf shed_upload.tar.gz
112 test-data/empty.fasta
113 test-data/empty_nlstradamus.tabular
114 test-data/four_human_proteins.fasta
115 test-data/four_human_proteins.nlstradamus.tabular
100 tools/nlstradamus/README.rst 116 tools/nlstradamus/README.rst
101 tools/nlstradamus/nlstradamus.xml 117 tools/nlstradamus/nlstradamus.xml
102 tools/nlstradamus/tool_dependencies.xml 118 tools/nlstradamus/tool_dependencies.xml
103 test-data/four_human_proteins.fasta 119 test-data/four_human_proteins.fasta
104 test-data/four_human_proteins.nlstradamus.tabular
105 test-data/empty.fasta
106 test-data/empty_nlstradamus.tabular
107 120
108 121
109 Licence (MIT) 122 Licence (MIT)
110 ============= 123 =============
111 124