Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README.rst @ 24:ee10017fcd80 draft

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author peterjc
date Tue, 17 Sep 2013 12:06:15 -0400
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children 41a42022f815
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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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7
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8 * WoLF PSORT v0.2 from http://wolfpsort.org/
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9
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10 * PSORTb v3 from http://www.psort.org/downloads/index.html
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11
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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 (MIT open source licence).
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21
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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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25 Citation
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26 ========
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27
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28 If you use any of these Galaxy tools in work leading to a scientific
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29 publication, in addition to citing the invididual underlying tools, please cite:
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30
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31 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
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32 Galaxy tools and workflows for sequence analysis with applications
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33 in molecular plant pathology. PeerJ 1:e167
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34 http://dx.doi.org/10.7717/peerj.167
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35
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36 Full reference information is included in the help text for each tool.
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39 Requirements
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40 ============
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41
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42 First install those command line tools you wish to use the wrappers for:
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43
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44 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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45 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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46
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47 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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48 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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49
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50 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
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51 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
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52
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53 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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54 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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55 directory, run runWolfPsortSummary, and then change back to the original
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56 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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57
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58 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
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59 but put it on the path under the name hmmsearch2 (allowing it to co-exist
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60 with HMMER 3), or edit rlxr_motif.py accordingly.
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61
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62 Verify each of the tools is installed and working from the command line
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63 (when logged in as the Galaxy user if appropriate).
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64
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65
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66 Manual Installation
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67 ===================
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68
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69 1. Create a folder tools/protein_analysis under your Galaxy installation.
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70 This folder name is not critical, and can be changed if desired - you
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71 must update the paths used in tool_conf.xml to match.
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72
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73 2. Copy/move the following files (from this archive) there:
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74
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75 * tmhmm2.xml (Galaxy tool definition)
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76 * tmhmm2.py (Python wrapper script)
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77
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78 * signalp3.xml (Galaxy tool definition)
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79 * signalp3.py (Python wrapper script)
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80
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81 * promoter2.xml (Galaxy tool definition)
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82 * promoter2.py (Python wrapper script)
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83
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84 * psortb.xml (Galaxy tool definition)
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85 * psortb.py (Python wrapper script)
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86
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87 * wolf_psort.xml (Galaxy tool definition)
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88 * wolf_psort.py (Python wrapper script)
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89
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90 * rxlr_motifs.xml (Galaxy tool definition)
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91 * rxlr_motifs.py (Python script)
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92
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93 * seq_analysis_utils.py (shared Python code)
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94 * LICENCE
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95 * README.rst (this file)
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96
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97 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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98 also tool_conf.xml.sample (to run the tests) to include the new tools
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99 by adding::
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100
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101 <section name="Protein sequence analysis" id="protein_analysis">
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102 <tool file="protein_analysis/tmhmm2.xml" />
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103 <tool file="protein_analysis/signalp3.xml" />
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104 <tool file="protein_analysis/psortb.xml" />
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105 <tool file="protein_analysis/wolf_psort.xml" />
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106 <tool file="protein_analysis/rxlr_motifs.xml" />
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107 </section>
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108 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
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109 <tool file="protein_analysis/promoter2.xml" />
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110 </section>
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111
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112 Leave out the lines for any tools you do not wish to use in Galaxy.
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113
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114 4. Copy/move the test-data files (from this archive) to Galaxy's
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115 subfolder test-data.
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116
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117 5. Run the Galaxy functional tests for these new wrappers with::
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118
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119 ./run_functional_tests.sh -id tmhmm2
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120 ./run_functional_tests.sh -id signalp3
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121 ./run_functional_tests.sh -id Psortb
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122 ./run_functional_tests.sh -id rxlr_motifs
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123
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124 Alternatively, this should work (assuming you left the name and id as shown in
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125 the XML file tool_conf.xml.sample)::
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126
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127 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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128
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129 To check the section ID expected, use ./run_functional_tests.sh -list
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130
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131 6. Restart Galaxy and check the new tools are shown and work.
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133
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134 History
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135 =======
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136
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137 ======= ======================================================================
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138 Version Changes
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139 ------- ----------------------------------------------------------------------
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140 v0.0.1 - Initial release
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141 v0.0.2 - Corrected some typos in the help text
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142 - Renamed test output file to use Galaxy convention of *.tabular
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143 v0.0.3 - Check for tmhmm2 silent failures (no output)
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144 - Additional unit tests
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145 v0.0.4 - Ignore comment lines in tmhmm2 output.
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146 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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147 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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148 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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149 SignalP webservice.
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150 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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151 v0.0.9 - Added our RXLR motifs tool to the suite.
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152 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
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153 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
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154 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
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155 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
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156 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
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157 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
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158 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
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159 contributed by Konrad Paszkiewicz.
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160 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
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161 files accidentally included previously via a wildcard).
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162 v0.2.2 - Include missing test files.
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163 v0.2.3 - Added unit tests for WoLF PSORT.
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164 v0.2.4 - Added unit tests for Promoter 2
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165 v0.2.5 - Link to Tool Shed added to help text and this documentation.
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166 - More unit tests.
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167 - Fixed bug with RXLR tool and empty FASTA files.
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168 - Fixed typo in the RXLR tool help text.
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169 - Updated citation information (Cock et al. 2013).
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170 - Adopted standard MIT licence.
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171 - Use reStructuredText for this README file.
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172 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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173 ======= ======================================================================
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174
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175
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176 Developers
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177 ==========
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178
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179 This script and other tools are being developed on the following hg branches:
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180 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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181 http://bitbucket.org/peterjc/galaxy-central/src/tools
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182
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183 Development has now moved to a dedicated GitHub repository:
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184 https://github.com/peterjc/pico_galaxy/tree/master/tools
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185
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186 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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187 the following command from the Galaxy root folder::
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188
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189 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
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190
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191 This simplifies ensuring a consistent set of files is bundled each time,
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192 including all the relevant test files.