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1 Python re-implementation of predictNLS with Galaxy wrapper
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2 ==========================================================
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4 This Galaxy tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 The tool consists of a Galaxy interface definition (``predictnls.xml``), and a Python
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9 script (``predictnls.py``) which re-implements the command line tool predictNLS. This
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10 should match the behaviour of predictNLS v1.0.20 (July 2011), the current latest
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11 release from the Rost Lab, see http://rostlab.org and their paper:
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12
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13 Murat Cokol, Rajesh Nair, and Burkhard Rost.
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14 Finding nuclear localization signals.
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15 EMBO reports 1(5), 411–415, 2000
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16 http://dx.doi.org/10.1093/embo-reports/kvd092
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17
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18 This wrapper is available from the Galaxy Tool Shed at
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19 http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
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20
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21
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22 Automatic Installation
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23 ======================
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24
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25 This Galaxy tool is self contained, and so should install automatically via the
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26 Galaxy Tool Shed.
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27
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28
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29 Manual Installation
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30 ===================
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31
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32 There are just four files which should be moved under the Galaxy tools folder,
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33 e.g. in a ``tools/protein_analysis`` filter:
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34
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35 * ``predictlns.xml`` (the Galaxy tool definition)
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36 * ``predictlns.py`` (the Python script)
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37 * ``predictlns.txt`` (this README file)
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38 * ``My_NLS_list`` (the default set of NLS motifs from the Rost Lab)
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39
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40 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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41 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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42 it next to them. Just add the line::
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43
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44 <tool file="protein_analysis/predictnls.xml" />
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45
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46 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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47 under Galaxy's ``test-data/`` folder. Then::
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48
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49 ./run_tests.sh -id predictnls
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50
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51 That's it.
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52
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53
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54 History
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55 =======
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56
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57 ======= ======================================================================
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58 Version Changes
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59 ------- ----------------------------------------------------------------------
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60 v0.0.4 - Initial public release.
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61 v0.0.5 - Treat non-zero return codes as errors.
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62 v0.0.6 - Link to Tool Shed added to help text and this documentation.
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63 - Use reStructuredText for this README file.
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64 - Updated citation information (Cock et al. 2013).
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65 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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66 v0.0.7 - Tool definition now embeds citation information.
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67 v0.0.8 - Reorder XML elements (internal change only).
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68 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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69 ======= ======================================================================
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70
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71
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72 Developers
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73 ==========
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74
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75 This script and related tools were initially developed on the following hg branch:
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76 http://bitbucket.org/peterjc/galaxy-central/src/tools
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77
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78 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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79 Planemo commands (which requires you have set your Tool Shed access details in
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80 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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81
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82 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/
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83 ...
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84
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85 or::
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86
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87 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/
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88 ...
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89
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90 To just build and check the tar ball, use::
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91
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92 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/predictnls/
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93 ...
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94 $ tar -tzf shed_upload.tar.gz
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95 test-data/four_human_proteins.fasta
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96 test-data/four_human_proteins.predictnls.tabular
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97 tools/predictnls/My_NLS_list
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98 tools/predictnls/README.rst
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99 tools/predictnls/predictnls.py
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100 tools/predictnls/predictnls.xml
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101
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102
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103 Licence (GPL)
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104 =============
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105
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106 This tool is open source, licensed under the GNU GENERAL PUBLIC LICENSE
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107 version 3 (GNU v3), see http://www.gnu.org/licenses/gpl.html
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108
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109 The Python script is my reimplementation of the original Perl program from
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110 the Rost Lab, which was released under the GPL v3. Therefore, as I consider
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111 this to be a derivative work, this too is released under the GPL v3.
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112
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113 Please note that the ``My_NLS_list`` file should be an exact copy of the file of the
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114 same name included with ``predictnls-1.0.7.tar.gz`` to ``predictnls-1.0.20.tar.gz``
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115 inclusive (the list was extended in v1.0.7 in August 2010, see the change log
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116 included in those tar-balls), available from ftp://rostlab.org/predictnls/
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