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annotate tools/protein_analysis/README @ 3:f3b373a41f81

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Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:05:13 -0400
parents 6901298ac16c
children 81caef04ce8b
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1 This package contains Galaxy wrappers for two standalone command line protein
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2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological
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3 Sequence Analysis at the Technical University of Denmark,
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4 http://www.cbs.dtu.dk/cbs/
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6 To use these Galaxy wrappers you must first install the CBS command line
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7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for
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8 academic use.
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9
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10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights
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11 reserved. See the included LICENCE file for details.
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13 Installation
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14 ============
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16 1. Install the command line version of SignalP 3.0 and ensure it is on the
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17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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18
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19 2. Install the command line version of TMHMM 2.0 and ensure it is on the
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20 PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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21
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22 3. Create a folder tools/protein_analysis under your Galaxy installation.
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24 4. Copy/move the following files (from this archive) there:
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26 tmhmm2.xml (Galaxy tool definition)
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27 tmhmm2.py (Python wrapper script)
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28 signalp3.xml (Galaxy tool definition)
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29 signalp3.py (Python wrapper script)
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30 seq_analysis_utils.py (shared Python code)
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31 README (optional)
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32
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33 5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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34 also tool_conf.xml.sample (to run the tests) to include the two new tools
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35 by adding:
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36
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37 <section name="Protein sequence analysis" id="protein_analysis">
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38 <tool file="protein_analysis/tmhmm2.xml" />
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39 <tool file="protein_analysis/signalp3.xml" />
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40 </section>
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41
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42 6. Copy/move the following test files (from these archive) to Galaxy
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43 subfolder test-data:
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44
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45 four_human_proteins.fasta
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46 four_human_proteins_signalp3.tabular
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47 four_human_proteins_tmhmm2.tabular
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48 empty.fasta
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49 empty_tmhmm2.tabular
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50 empty_signalp3.tabular
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51
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52 7. Run the Galaxy functional tests for these new wrappers with:
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53
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54 ./run_functional_tests.sh -id tmhmm2
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55 ./run_functional_tests.sh -id signalp3
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56
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57 Alternatively, this should work (assuming you left the name and id as shown in
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58 the XML file tool_conf.xml.sample):
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59
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60 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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61
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62 8. Restart Galaxy and check the new tools are shown and work.
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65 History
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66 =======
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67
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68 v0.0.1 - Initial release
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69 v0.0.2 - Corrected some typos in the help text
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70 - Renamed test output file to use Galaxy convention of *.tabular
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71 v0.0.3 - Check for tmhmm2 silent failures (no output)
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72 - Additional unit tests
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73 v0.0.4 - Ignore comment lines in tmhmm2 output.
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74 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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75 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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77 Developers
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78 ==========
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79
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80 This script and other tools are being developed on the following hg branch:
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81 http://bitbucket.org/peterjc/galaxy-central/src/tools
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82
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83 This incorporates the previously used hg branch:
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84 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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85
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86 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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87 the following command from the Galaxy root folder:
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89 tar -czf tmhmm_and_signalp.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular
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91 Check this worked:
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92
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93 $ tar -tzf tmhmm_and_signalp.tar.gz
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94 tools/protein_analysis/LICENSE
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95 tools/protein_analysis/README
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96 tools/protein_analysis/suite_config.xml
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97 tools/protein_analysis/seq_analysis_utils.py
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98 tools/protein_analysis/signalp3.xml
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99 tools/protein_analysis/signalp3.py
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100 tools/protein_analysis/tmhmm2.xml
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101 tools/protein_analysis/tmhmm2.py
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102 test-data/four_human_proteins.fasta
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103 test-data/four_human_proteins.signalp3.tabular
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104 test-data/four_human_proteins.tmhmm2.tabular
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105 test-data/empty.fasta
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106 test-data/empty_tmhmm2.tabular
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107 test-data/empty_signalp3.tabular