Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 9:9a9971a1e55e draft

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Uploaded v0.2.0a (As before but adding missing RXLR HMM file)
author peterjc
date Wed, 27 Mar 2013 11:15:44 -0400
parents 391a142c1e60
children 7c1eda453701
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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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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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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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17 These wrappers are copyright 2010-2012 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 See the included LICENCE file for details (an MIT style open source licence).
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21 Requirements
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22 ============
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23
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24 First install those command line tools you wish to use the wrappers for:
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26 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
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27 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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29 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
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30 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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32 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
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33 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
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35 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
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36 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
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37 directory, run runWolfPsortSummary, and then change back to the original
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38 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
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40 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
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41 but put it on the path under the name hmmsearch2 (allowing it to co-exist
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42 with HMMER 3), or edit rlxr_motif.py accordingly.
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43
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44 Verify each of the tools is installed and working from the command line
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45 (when logged in as the Galaxy user if appropriate).
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47 Manual Installation
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48 ===================
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49
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50 1. Create a folder tools/protein_analysis under your Galaxy installation.
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51 This folder name is not critical, and can be changed if desired - you
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52 must update the paths used in tool_conf.xml to match.
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53
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54 2. Copy/move the following files (from this archive) there:
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56 tmhmm2.xml (Galaxy tool definition)
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57 tmhmm2.py (Python wrapper script)
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58
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59 signalp3.xml (Galaxy tool definition)
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60 signalp3.py (Python wrapper script)
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62 promoter2.xml (Galaxy tool definition)
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63 promoter2.py (Python wrapper script)
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64
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65 psortb.xml (Galaxy tool definition)
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66 psortb.py (Python wrapper script)
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67
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68 wolf_psort.xml (Galaxy tool definition)
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69 wolf_psort.py (Python wrapper script)
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71 rxlr_motifs.xml (Galaxy tool definition)
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72 rxlr_motifs.py (Python script)
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74 seq_analysis_utils.py (shared Python code)
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75 LICENCE
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76 README (this file)
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77
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78 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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79 also tool_conf.xml.sample (to run the tests) to include the new tools
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80 by adding:
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81
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82 <section name="Protein sequence analysis" id="protein_analysis">
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83 <tool file="protein_analysis/tmhmm2.xml" />
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84 <tool file="protein_analysis/signalp3.xml" />
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85 <tool file="protein_analysis/psortb.xml" />
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86 <tool file="protein_analysis/wolf_psort.xml" />
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87 <tool file="protein_analysis/rxlr_motifs.xml" />
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88 </section>
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89 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
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90 <tool file="protein_analysis/promoter2.xml" />
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91 </section>
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92
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93 Leave out the lines for any tools you do not wish to use in Galaxy.
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94
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95 4. Copy/move the following test files (from these archive) to Galaxy
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96 subfolder test-data:
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98 four_human_proteins.fasta
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99 four_human_proteins_signalp3.tabular
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100 four_human_proteins_tmhmm2.tabular
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101 empty.fasta
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102 empty_tmhmm2.tabular
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103 empty_signalp3.tabular
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104 k12_ten_proteins.fasta
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105 k12_ten_proteins_psortb_p_terse.tabular
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106
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107 5. Run the Galaxy functional tests for these new wrappers with:
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108
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109 ./run_functional_tests.sh -id tmhmm2
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110 ./run_functional_tests.sh -id signalp3
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111 ./run_functional_tests.sh -id Psortb
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112 ./run_functional_tests.sh -id rxlr_motifs
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113
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114 Alternatively, this should work (assuming you left the name and id as shown in
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115 the XML file tool_conf.xml.sample):
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116
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117 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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118
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119 To check the section ID expected, use ./run_functional_tests.sh -list
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120
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121 6. Restart Galaxy and check the new tools are shown and work.
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124 History
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125 =======
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127 v0.0.1 - Initial release
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128 v0.0.2 - Corrected some typos in the help text
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129 - Renamed test output file to use Galaxy convention of *.tabular
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130 v0.0.3 - Check for tmhmm2 silent failures (no output)
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131 - Additional unit tests
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132 v0.0.4 - Ignore comment lines in tmhmm2 output.
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133 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
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134 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
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135 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
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136 SignalP webservice.
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137 v0.0.8 - Added WoLF PSORT wrapper to the suite.
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138 v0.0.9 - Added our RXLR motifs tool to the suite.
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139 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
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140 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
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141 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
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142 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
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143 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
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144 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
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145 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
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146 contributed by Konrad Paszkiewicz.
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147
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148
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149 Developers
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150 ==========
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151
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152 This script and other tools are being developed on the following hg branch:
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153 http://bitbucket.org/peterjc/galaxy-central/src/tools
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154
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155 This incorporates the previously used hg branch:
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156 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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157
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158 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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159 the following command from the Galaxy root folder:
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160
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161 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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162
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163 Check this worked:
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164
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165 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz
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166 tools/protein_analysis/LICENSE
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167 tools/protein_analysis/README
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168 tools/protein_analysis/suite_config.xml
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169 tools/protein_analysis/seq_analysis_utils.py
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170 tools/protein_analysis/signalp3.xml
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171 tools/protein_analysis/signalp3.py
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172 tools/protein_analysis/tmhmm2.xml
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173 tools/protein_analysis/tmhmm2.py
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174 tools/protein_analysis/promoter2.xml
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175 tools/protein_analysis/promoter2.py
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176 tools/protein_analysis/psortb.xml
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177 tools/protein_analysis/psortb.py
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178 tools/protein_analysis/wolf_psort.xml
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179 tools/protein_analysis/wolf_psort.py
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180 tools/protein_analysis/rxlr_motifs.xml
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181 tools/protein_analysis/rxrl_motifs.py
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182 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
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183 test-data/four_human_proteins.fasta
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184 test-data/four_human_proteins.signalp3.tabular
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185 test-data/four_human_proteins.tmhmm2.tabular
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186 test-data/empty.fasta
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187 test-data/empty_tmhmm2.tabular
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188 test-data/empty_signalp3.tabular
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189 test-data/k12_ten_proteins.fasta
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190 test-data/k12_ten_proteins_psortb_p_terse.tabular