Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/README.rst @ 17:e6cc27d182a8 draft
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author | peterjc |
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date | Fri, 21 Nov 2014 08:19:09 -0500 |
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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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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 (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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24 |
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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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37 |
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38 |
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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 |
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60 co-exist 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 include the |
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98 new tools by adding:: |
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99 |
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100 <section name="Protein sequence analysis" id="protein_analysis"> |
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101 <tool file="protein_analysis/tmhmm2.xml" /> |
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102 <tool file="protein_analysis/signalp3.xml" /> |
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103 <tool file="protein_analysis/psortb.xml" /> |
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104 <tool file="protein_analysis/wolf_psort.xml" /> |
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105 <tool file="protein_analysis/rxlr_motifs.xml" /> |
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106 </section> |
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107 <section name="Nucleotide sequence analysis" id="nucleotide_analysis"> |
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108 <tool file="protein_analysis/promoter2.xml" /> |
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109 </section> |
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110 |
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111 Leave out the lines for any tools you do not wish to use in Galaxy. |
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112 |
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113 4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's |
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114 subfolder ``test-data/``. |
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115 |
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116 5. Run the Galaxy functional tests for these new wrappers with:: |
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117 |
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118 $ ./run_tests.sh -id tmhmm2 |
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119 $ ./run_tests.sh -id signalp3 |
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120 $ ./run_tests.sh -id Psortb |
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121 $ ./run_tests.sh -id rxlr_motifs |
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122 |
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123 Alternatively, this should work (assuming you left the seciont name and id |
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124 as shown above in your XML file ``tool_conf.xml``):: |
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125 |
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126 $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis |
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127 |
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128 To check the section ID expected, use: |
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129 |
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130 $ ./run_tests.sh -list |
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131 |
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132 6. Restart Galaxy and check the new tools are shown and work. |
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133 |
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134 |
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135 History |
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136 ======= |
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137 |
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138 ======= ====================================================================== |
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139 Version Changes |
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140 ------- ---------------------------------------------------------------------- |
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141 v0.0.1 - Initial release |
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142 v0.0.2 - Corrected some typos in the help text |
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143 - Renamed test output file to use Galaxy convention of ``*.tabular`` |
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144 v0.0.3 - Check for tmhmm2 silent failures (no output) |
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145 - Additional unit tests |
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146 v0.0.4 - Ignore comment lines in tmhmm2 output. |
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147 v0.0.5 - Explicitly request tmhmm short output (may not be the default) |
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148 v0.0.6 - Improvement to how sub-jobs are run (should be faster) |
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149 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the |
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150 SignalP webservice. |
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151 v0.0.8 - Added WoLF PSORT wrapper to the suite. |
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152 v0.0.9 - Added our RXLR motifs tool to the suite. |
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153 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) |
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154 - Support Galaxy's ``<parallelism>`` tag for SignalP, TMHMM & Promoter |
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155 v0.1.1 - Fixed an error in the header of the tabular output from Promoter |
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156 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors |
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157 - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4) |
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158 v0.1.3 - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed |
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159 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work |
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160 contributed by Konrad Paszkiewicz. |
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161 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray |
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162 files accidentally included previously via a wildcard). |
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163 v0.2.2 - Include missing test files. |
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164 v0.2.3 - Added unit tests for WoLF PSORT. |
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165 v0.2.4 - Added unit tests for Promoter 2 |
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166 v0.2.5 - Link to Tool Shed added to help text and this documentation. |
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167 - More unit tests. |
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168 - Fixed bug with RXLR tool and empty FASTA files. |
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169 - Fixed typo in the RXLR tool help text. |
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170 - Updated citation information (Cock et al. 2013). |
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171 - Adopted standard MIT licence. |
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172 - Use reStructuredText for this README file. |
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173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. |
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175 - Updated the ``suite_config.xml`` file (overdue). |
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176 - Tool definition now embeds citation information. |
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177 ======= ====================================================================== |
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178 |
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179 |
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180 Developers |
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181 ========== |
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182 |
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183 This script and other tools were initially developed on the following hg branches: |
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184 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis |
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185 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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186 |
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187 Development has now moved to a dedicated GitHub repository: |
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188 https://github.com/peterjc/pico_galaxy/tree/master/tools |
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189 |
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190 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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191 the following command from the Galaxy root folder:: |
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192 |
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193 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh |
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194 |
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195 This simplifies ensuring a consistent set of files is bundled each time, |
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196 including all the relevant test files. |