Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 18:2b35b5c4b7f4 draft

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Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
author peterjc
date Fri, 10 May 2013 07:48:26 -0400
parents af3174637834
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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, THMHMM 2.0, Promoter 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 * PSORTb v3 from http://www.psort.org/downloads/index.html
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12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
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14 To use these Galaxy wrappers you must first install the command line tools.
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15 At the time of writing they are all free for academic use, or open source.
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16
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17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
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18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
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20 See the included LICENCE file for details (an MIT style open source licence).
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22 The wrappers are available from the Galaxy Tool Shed
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23 http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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26 Requirements
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27 ============
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28
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29 First install those command line tools you wish to use the wrappers for:
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31 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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32 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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34 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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35 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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37 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
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38 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
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39
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40 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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41 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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42 directory, run runWolfPsortSummary, and then change back to the original
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43 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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45 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
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46 but put it on the path under the name hmmsearch2 (allowing it to co-exist
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47 with HMMER 3), or edit rlxr_motif.py accordingly.
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48
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49 Verify each of the tools is installed and working from the command line
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50 (when logged in as the Galaxy user if appropriate).
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53 Manual Installation
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54 ===================
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55
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56 1. Create a folder tools/protein_analysis under your Galaxy installation.
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57 This folder name is not critical, and can be changed if desired - you
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58 must update the paths used in tool_conf.xml to match.
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59
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60 2. Copy/move the following files (from this archive) there:
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61
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62 tmhmm2.xml (Galaxy tool definition)
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63 tmhmm2.py (Python wrapper script)
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64
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65 signalp3.xml (Galaxy tool definition)
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66 signalp3.py (Python wrapper script)
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68 promoter2.xml (Galaxy tool definition)
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69 promoter2.py (Python wrapper script)
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70
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71 psortb.xml (Galaxy tool definition)
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72 psortb.py (Python wrapper script)
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73
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74 wolf_psort.xml (Galaxy tool definition)
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75 wolf_psort.py (Python wrapper script)
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77 rxlr_motifs.xml (Galaxy tool definition)
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78 rxlr_motifs.py (Python script)
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79
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80 seq_analysis_utils.py (shared Python code)
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81 LICENCE
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82 README (this file)
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83
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84 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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85 also tool_conf.xml.sample (to run the tests) to include the new tools
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86 by adding:
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87
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88 <section name="Protein sequence analysis" id="protein_analysis">
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89 <tool file="protein_analysis/tmhmm2.xml" />
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90 <tool file="protein_analysis/signalp3.xml" />
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91 <tool file="protein_analysis/psortb.xml" />
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92 <tool file="protein_analysis/wolf_psort.xml" />
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93 <tool file="protein_analysis/rxlr_motifs.xml" />
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94 </section>
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95 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
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96 <tool file="protein_analysis/promoter2.xml" />
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97 </section>
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98
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99 Leave out the lines for any tools you do not wish to use in Galaxy.
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100
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101 4. Copy/move the test-data files (from this archive) to Galaxy's
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102 subfolder test-data.
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103
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104 5. Run the Galaxy functional tests for these new wrappers with:
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105
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106 ./run_functional_tests.sh -id tmhmm2
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107 ./run_functional_tests.sh -id signalp3
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108 ./run_functional_tests.sh -id Psortb
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109 ./run_functional_tests.sh -id rxlr_motifs
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110
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111 Alternatively, this should work (assuming you left the name and id as shown in
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112 the XML file tool_conf.xml.sample):
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113
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114 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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116 To check the section ID expected, use ./run_functional_tests.sh -list
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117
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118 6. Restart Galaxy and check the new tools are shown and work.
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121 History
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122 =======
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124 v0.0.1 - Initial release
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125 v0.0.2 - Corrected some typos in the help text
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126 - Renamed test output file to use Galaxy convention of *.tabular
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127 v0.0.3 - Check for tmhmm2 silent failures (no output)
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128 - Additional unit tests
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129 v0.0.4 - Ignore comment lines in tmhmm2 output.
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130 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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131 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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132 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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133 SignalP webservice.
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134 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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135 v0.0.9 - Added our RXLR motifs tool to the suite.
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136 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
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137 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
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138 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
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139 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
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140 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
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141 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
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142 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
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143 contributed by Konrad Paszkiewicz.
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144 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
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145 files accidentally included previously via a wildcard).
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146 v0.2.2 - Include missing test files.
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a705202ae2a7 Uploaded v0.2.3, adds unit tests for WoLF PSORT
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147 v0.2.3 - Added unit tests for WoLF PSORT.
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1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
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148 v0.2.4 - Added unit tests for Promoter 2
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af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
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149 v0.2.5 - Link to Tool Shed added to help text and this documentation.
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2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
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150 - More unit tests.
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151 - Fixed bug with RXLR tool and empty FASTA files.
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152
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153
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154
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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155 Developers
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156 ==========
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157
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158 This script and other tools are being developed on the following hg branch:
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159 http://bitbucket.org/peterjc/galaxy-central/src/tools
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160
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161 This incorporates the previously used hg branch:
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162 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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163
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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164 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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165 the following command from the Galaxy root folder:
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166
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167 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
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168
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169 This simplifies ensuring a consistent set of files is bundled each time,
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170 including all the relevant test files.