Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 6:39a6e46cdda3

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Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:41:38 -0400
parents ef7ceca37e3f
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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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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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10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
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11
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12 To use these Galaxy wrappers you must first install the command line tools.
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13 At the time of writing they are all free for academic use.
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15 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute
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16 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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17 See the included LICENCE file for details.
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19 Requirements
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20 ============
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21
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22 First install those command line tools you wish to use the wrappers for:
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24 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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25 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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27 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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28 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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30 3. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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31 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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32 directory, run runWolfPsortSummary, and then change back to the original
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33 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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35 4. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
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36 but put it on the path under the name hmmsearch2 (allowing it to co-exist
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37 with HMMER 3), or edit rlxr_motif.py accordingly.
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39 Verify each of the tools is installed and working from the command line
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40 (when logged in at the Galaxy user if appropriate).
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42 Installation
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43 ============
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44
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45 1. Create a folder tools/protein_analysis under your Galaxy installation.
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47 2. Copy/move the following files (from this archive) there:
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49 tmhmm2.xml (Galaxy tool definition)
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50 tmhmm2.py (Python wrapper script)
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52 signalp3.xml (Galaxy tool definition)
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53 signalp3.py (Python wrapper script)
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55 wolf_psort.xml (Galaxy tool definition)
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56 wolf_psort.py (Python wrapper script)
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57
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58 rxlr_motifs.xml (Galaxy tool definition)
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59 rxlr_motifs.py (Python script)
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60
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61 seq_analysis_utils.py (shared Python code)
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62 README (optional)
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63
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64 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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65 also tool_conf.xml.sample (to run the tests) to include the new tools
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66 by adding:
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68 <section name="Protein sequence analysis" id="protein_analysis">
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69 <tool file="protein_analysis/tmhmm2.xml" />
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70 <tool file="protein_analysis/signalp3.xml" />
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71 <tool file="protein_analysis/wolf_psort.xml" />
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72 <tool file="protein_analysis/rxlr_motifs.xml" />
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73 </section>
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75 Leave out the lines for any tools you do not wish to use in Galaxy.
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76
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77 4. Copy/move the following test files (from these archive) to Galaxy
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78 subfolder test-data:
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80 four_human_proteins.fasta
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81 four_human_proteins_signalp3.tabular
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82 four_human_proteins_tmhmm2.tabular
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83 empty.fasta
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84 empty_tmhmm2.tabular
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85 empty_signalp3.tabular
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86
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87 5. Run the Galaxy functional tests for these new wrappers with:
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88
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89 ./run_functional_tests.sh -id tmhmm2
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90 ./run_functional_tests.sh -id signalp3
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91
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92 Alternatively, this should work (assuming you left the name and id as shown in
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93 the XML file tool_conf.xml.sample):
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94
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95 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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96
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97 6. Restart Galaxy and check the new tools are shown and work.
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100 History
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101 =======
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102
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103 v0.0.1 - Initial release
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104 v0.0.2 - Corrected some typos in the help text
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105 - Renamed test output file to use Galaxy convention of *.tabular
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106 v0.0.3 - Check for tmhmm2 silent failures (no output)
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107 - Additional unit tests
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108 v0.0.4 - Ignore comment lines in tmhmm2 output.
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109 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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110 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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111 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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112 SignalP webservice.
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113 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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114 v0.0.9 - Added our RXLR motifs tool to the suite.
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117 Developers
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118 ==========
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119
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120 This script and other tools are being developed on the following hg branch:
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121 http://bitbucket.org/peterjc/galaxy-central/src/tools
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123 This incorporates the previously used hg branch:
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124 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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126 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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127 the following command from the Galaxy root folder:
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129 tar -czf tmhmm_signalp_etc.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 tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular
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131 Check this worked:
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133 $ tar -tzf tmhmm_signalp_etc.tar.gz
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134 tools/protein_analysis/LICENSE
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135 tools/protein_analysis/README
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136 tools/protein_analysis/suite_config.xml
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137 tools/protein_analysis/seq_analysis_utils.py
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138 tools/protein_analysis/signalp3.xml
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139 tools/protein_analysis/signalp3.py
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140 tools/protein_analysis/tmhmm2.xml
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141 tools/protein_analysis/tmhmm2.py
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142 tools/protein_analysis/wolf_psort.xml
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143 tools/protein_analysis/wolf_psort.py
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144 tools/protein_analysis/rxlr_motifs.xml
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145 tools/protein_analysis/rxrl_motifs.py
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146 test-data/four_human_proteins.fasta
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147 test-data/four_human_proteins.signalp3.tabular
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148 test-data/four_human_proteins.tmhmm2.tabular
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149 test-data/empty.fasta
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150 test-data/empty_tmhmm2.tabular
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151 test-data/empty_signalp3.tabular