Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 10:7c1eda453701 draft

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Uploaded revised v0.2.0 with clearer acknowledgement of contributors
author peterjc
date Wed, 03 Apr 2013 10:31:27 -0400
parents 9a9971a1e55e
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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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9
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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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13
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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 Requirements
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23 ============
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24
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25 First install those command line tools you wish to use the wrappers for:
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27 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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28 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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30 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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31 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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32
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33 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
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34 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
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36 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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37 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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38 directory, run runWolfPsortSummary, and then change back to the original
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39 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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41 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
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42 but put it on the path under the name hmmsearch2 (allowing it to co-exist
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43 with HMMER 3), or edit rlxr_motif.py accordingly.
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44
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45 Verify each of the tools is installed and working from the command line
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46 (when logged in as the Galaxy user if appropriate).
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48 Manual Installation
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49 ===================
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50
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51 1. Create a folder tools/protein_analysis under your Galaxy installation.
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52 This folder name is not critical, and can be changed if desired - you
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53 must update the paths used in tool_conf.xml to match.
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54
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55 2. Copy/move the following files (from this archive) there:
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57 tmhmm2.xml (Galaxy tool definition)
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58 tmhmm2.py (Python wrapper script)
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59
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60 signalp3.xml (Galaxy tool definition)
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61 signalp3.py (Python wrapper script)
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63 promoter2.xml (Galaxy tool definition)
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64 promoter2.py (Python wrapper script)
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65
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66 psortb.xml (Galaxy tool definition)
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67 psortb.py (Python wrapper script)
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68
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69 wolf_psort.xml (Galaxy tool definition)
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70 wolf_psort.py (Python wrapper script)
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72 rxlr_motifs.xml (Galaxy tool definition)
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73 rxlr_motifs.py (Python script)
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75 seq_analysis_utils.py (shared Python code)
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76 LICENCE
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77 README (this file)
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78
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79 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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80 also tool_conf.xml.sample (to run the tests) to include the new tools
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81 by adding:
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82
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83 <section name="Protein sequence analysis" id="protein_analysis">
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84 <tool file="protein_analysis/tmhmm2.xml" />
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85 <tool file="protein_analysis/signalp3.xml" />
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86 <tool file="protein_analysis/psortb.xml" />
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87 <tool file="protein_analysis/wolf_psort.xml" />
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88 <tool file="protein_analysis/rxlr_motifs.xml" />
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89 </section>
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90 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
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91 <tool file="protein_analysis/promoter2.xml" />
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92 </section>
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93
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94 Leave out the lines for any tools you do not wish to use in Galaxy.
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95
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96 4. Copy/move the following test files (from these archive) to Galaxy
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97 subfolder test-data:
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99 four_human_proteins.fasta
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100 four_human_proteins_signalp3.tabular
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101 four_human_proteins_tmhmm2.tabular
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102 empty.fasta
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103 empty_tmhmm2.tabular
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104 empty_signalp3.tabular
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105 k12_ten_proteins.fasta
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106 k12_ten_proteins_psortb_p_terse.tabular
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107
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108 5. Run the Galaxy functional tests for these new wrappers with:
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109
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110 ./run_functional_tests.sh -id tmhmm2
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111 ./run_functional_tests.sh -id signalp3
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112 ./run_functional_tests.sh -id Psortb
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113 ./run_functional_tests.sh -id rxlr_motifs
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114
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115 Alternatively, this should work (assuming you left the name and id as shown in
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116 the XML file tool_conf.xml.sample):
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117
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118 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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119
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120 To check the section ID expected, use ./run_functional_tests.sh -list
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121
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122 6. Restart Galaxy and check the new tools are shown and work.
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125 History
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126 =======
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127
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128 v0.0.1 - Initial release
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129 v0.0.2 - Corrected some typos in the help text
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130 - Renamed test output file to use Galaxy convention of *.tabular
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131 v0.0.3 - Check for tmhmm2 silent failures (no output)
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132 - Additional unit tests
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133 v0.0.4 - Ignore comment lines in tmhmm2 output.
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134 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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135 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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136 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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137 SignalP webservice.
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138 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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139 v0.0.9 - Added our RXLR motifs tool to the suite.
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140 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
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141 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
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142 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
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143 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
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144 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
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145 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
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146 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
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147 contributed by Konrad Paszkiewicz.
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148
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149
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150 Developers
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151 ==========
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152
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153 This script and other tools are being developed on the following hg branch:
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154 http://bitbucket.org/peterjc/galaxy-central/src/tools
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155
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156 This incorporates the previously used hg branch:
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157 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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158
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159 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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160 the following command from the Galaxy root folder:
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161
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162 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/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/psortb.xml tools/protein_analysis/psortb.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 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular test-data/k12_ten_proteins.fasta test-data/k12_ten_proteins_psortb_p_terse.tabular
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163
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164 Check this worked:
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165
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166 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz
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167 tools/protein_analysis/LICENSE
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168 tools/protein_analysis/README
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169 tools/protein_analysis/suite_config.xml
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170 tools/protein_analysis/seq_analysis_utils.py
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171 tools/protein_analysis/signalp3.xml
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172 tools/protein_analysis/signalp3.py
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173 tools/protein_analysis/tmhmm2.xml
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174 tools/protein_analysis/tmhmm2.py
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175 tools/protein_analysis/promoter2.xml
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176 tools/protein_analysis/promoter2.py
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177 tools/protein_analysis/psortb.xml
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178 tools/protein_analysis/psortb.py
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179 tools/protein_analysis/wolf_psort.xml
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180 tools/protein_analysis/wolf_psort.py
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181 tools/protein_analysis/rxlr_motifs.xml
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182 tools/protein_analysis/rxrl_motifs.py
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183 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
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184 test-data/four_human_proteins.fasta
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185 test-data/four_human_proteins.signalp3.tabular
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186 test-data/four_human_proteins.tmhmm2.tabular
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187 test-data/empty.fasta
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188 test-data/empty_tmhmm2.tabular
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189 test-data/empty_signalp3.tabular
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190 test-data/k12_ten_proteins.fasta
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191 test-data/k12_ten_proteins_psortb_p_terse.tabular