annotate tools/protein_analysis/README @ 5:ef7ceca37e3f

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author peterjc
date Tue, 07 Jun 2011 17:40:55 -0400
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1 This package contains Galaxy wrappers for a selection of standalone command
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2 line protein analysis tools:
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3
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4 * SignalP 3.0 and THMHMM 2.0, from the Center for Biological
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5 Sequence Analysis at the Technical University of Denmark,
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6 http://www.cbs.dtu.dk/cbs/
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8 * WoLF PSORT v0.2 from http://wolfpsort.org/
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9
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10 To use these Galaxy wrappers you must first install the command line tools.
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11 At the time of writing they are all free for academic use.
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12
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13 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute
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14 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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15 See the included LICENCE file for details.
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17 Requirements
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18 ============
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19
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20 First install those command line tools you wish to use the wrappers for:
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21
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22 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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23 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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25 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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26 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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27
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28 3. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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29 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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30 directory, run runWolfPsortSummary, and then change back to the original
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31 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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33 Verify each of the tools is installed and working from the command line
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34 (when logged in at the Galaxy user if appropriate).
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36 Installation
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37 ============
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38
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39 1. Create a folder tools/protein_analysis under your Galaxy installation.
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40
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41 2. Copy/move the following files (from this archive) there:
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42
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43 tmhmm2.xml (Galaxy tool definition)
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44 tmhmm2.py (Python wrapper script)
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45
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46 signalp3.xml (Galaxy tool definition)
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47 signalp3.py (Python wrapper script)
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48
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49 wolf_psort.xml (Galaxy tool definition)
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50 wolf_psort.py (Python wrapper script)
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51
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52 seq_analysis_utils.py (shared Python code)
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53 README (optional)
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54
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55 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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56 also tool_conf.xml.sample (to run the tests) to include the new tools
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57 by adding:
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58
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59 <section name="Protein sequence analysis" id="protein_analysis">
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60 <tool file="protein_analysis/tmhmm2.xml" />
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61 <tool file="protein_analysis/signalp3.xml" />
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62 <tool file="protein_analysis/wolf_psort.xml" />
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63 </section>
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64
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65 Leave out the lines for any tools you do not wish to use in Galaxy.
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66
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67 4. Copy/move the following test files (from these archive) to Galaxy
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68 subfolder test-data:
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69
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70 four_human_proteins.fasta
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71 four_human_proteins_signalp3.tabular
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72 four_human_proteins_tmhmm2.tabular
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73 empty.fasta
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74 empty_tmhmm2.tabular
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75 empty_signalp3.tabular
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76
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77 5. Run the Galaxy functional tests for these new wrappers with:
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78
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79 ./run_functional_tests.sh -id tmhmm2
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80 ./run_functional_tests.sh -id signalp3
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81
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82 Alternatively, this should work (assuming you left the name and id as shown in
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83 the XML file tool_conf.xml.sample):
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84
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85 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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86
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87 6. Restart Galaxy and check the new tools are shown and work.
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90 History
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91 =======
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92
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93 v0.0.1 - Initial release
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94 v0.0.2 - Corrected some typos in the help text
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95 - Renamed test output file to use Galaxy convention of *.tabular
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96 v0.0.3 - Check for tmhmm2 silent failures (no output)
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97 - Additional unit tests
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98 v0.0.4 - Ignore comment lines in tmhmm2 output.
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99 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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100 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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101 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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102 SignalP webservice.
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103 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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106 Developers
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107 ==========
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108
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109 This script and other tools are being developed on the following hg branch:
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110 http://bitbucket.org/peterjc/galaxy-central/src/tools
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111
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112 This incorporates the previously used hg branch:
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113 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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115 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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116 the following command from the Galaxy root folder:
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117
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118 tar -czf tmhmm_signalp_wolfpsort.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 tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular
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120 Check this worked:
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121
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122 $ tar -tzf tmhmm_signalp_wolfpsort.tar.gz
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123 tools/protein_analysis/LICENSE
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124 tools/protein_analysis/README
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125 tools/protein_analysis/suite_config.xml
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126 tools/protein_analysis/seq_analysis_utils.py
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127 tools/protein_analysis/signalp3.xml
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128 tools/protein_analysis/signalp3.py
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129 tools/protein_analysis/tmhmm2.xml
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130 tools/protein_analysis/tmhmm2.py
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131 tools/protein_analysis/wolf_psort.xml
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132 tools/protein_analysis/wolf_psort.py
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133 test-data/four_human_proteins.fasta
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134 test-data/four_human_proteins.signalp3.tabular
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135 test-data/four_human_proteins.tmhmm2.tabular
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136 test-data/empty.fasta
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137 test-data/empty_tmhmm2.tabular
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138 test-data/empty_signalp3.tabular