Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/README.rst @ 31:3c9bbbc6cbbe draft
v0.2.11 take two; removed tabs in README file
author | peterjc |
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date | Thu, 21 Sep 2017 11:23:01 -0400 |
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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 |
26
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17 These wrappers are copyright 2010-2015 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 |
25 | 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 |
25 | 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 |
25 | 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 |
25 | 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) |
25 | 59 but put it on the path under the name ``hmmsearch2`` (allowing it to |
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 |
25 | 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 |
25 | 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 |
25 | 75 * ``tmhmm2.xml`` (Galaxy tool definition) |
76 * ``tmhmm2.py`` (Python wrapper script) | |
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77 |
25 | 78 * ``signalp3.xml`` (Galaxy tool definition) |
79 * ``signalp3.py`` (Python wrapper script) | |
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80 |
25 | 81 * ``promoter2.xml`` (Galaxy tool definition) |
82 * ``promoter2.py`` (Python wrapper script) | |
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83 |
25 | 84 * ``psortb.xml`` (Galaxy tool definition) |
85 * ``psortb.py`` (Python wrapper script) | |
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86 |
25 | 87 * ``wolf_psort.xml`` (Galaxy tool definition) |
88 * ``wolf_psort.py`` (Python wrapper script) | |
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89 |
25 | 90 * ``rxlr_motifs.xml`` (Galaxy tool definition) |
91 * ``rxlr_motifs.py`` (Python script) | |
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92 |
25 | 93 * ``seq_analysis_utils.py`` (shared Python code) |
94 * ``LICENCE`` | |
95 * ``README.rst`` (this file) | |
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96 |
25 | 97 3. Edit your Galaxy conjuration file ``tool_conf.xml`` to include the |
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 |
25 | 113 4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's |
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 |
25 | 118 $ ./run_tests.sh -id tmhmm2 |
119 $ ./run_tests.sh -id signalp3 | |
120 $ ./run_tests.sh -id Psortb | |
121 $ ./run_tests.sh -id rxlr_motifs | |
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122 |
25 | 123 Alternatively, this should work (assuming you left the seciont name and id |
124 as shown above in your XML file ``tool_conf.xml``):: | |
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125 |
25 | 126 $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis |
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127 |
25 | 128 To check the section ID expected, use: |
129 | |
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 |
25 | 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) |
25 | 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 |
25 | 157 - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4) |
158 v0.1.3 - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed | |
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159 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work |
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160 contributed by Konrad Paszkiewicz. |
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161 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray |
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162 files accidentally included previously via a wildcard). |
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163 v0.2.2 - Include missing test files. |
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164 v0.2.3 - Added unit tests for WoLF PSORT. |
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165 v0.2.4 - Added unit tests for Promoter 2 |
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166 v0.2.5 - Link to Tool Shed added to help text and this documentation. |
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167 - More unit tests. |
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168 - Fixed bug with RXLR tool and empty FASTA files. |
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169 - Fixed typo in the RXLR tool help text. |
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170 - Updated citation information (Cock et al. 2013). |
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171 - Adopted standard MIT licence. |
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172 - Use reStructuredText for this README file. |
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173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
25 | 174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. |
175 - Updated the ``suite_config.xml`` file (overdue). | |
176 - Tool definition now embeds citation information. | |
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177 v0.2.7 - Style cleanup in Python scripts using ``pep8``. |
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178 v0.2.8 - Reorder XML elements (internal change only). |
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179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
28 | 180 - Record version of Promoter 2 via ``<version_command>``. |
29 | 181 v0.2.9 - Further style cleanup in Python scripts (internal change only). |
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182 v0.2.10 - Style cleanup in Python scripts using ``flake8``. |
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183 - Record TMHMM and SignalP wrapper version via ``<version_command>``. |
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184 - Python 3 compatible print function and exception handling. |
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185 - Python 3 compatible subprocess calling. |
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186 - Removed obsolete ``suite_config.xml`` file. |
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187 v0.2.11 - Updated RXLR tool dependencies to get HMMER2 via BioConda. |
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188 - Use ``<command detect_errors="aggressive">`` (internal change only). |
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189 - Single quote command line arguments (internal change only). |
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190 - Record WoLF PSORT wrapper version via ``<version_command>``. |
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191 - Fix error handling in SignalP wrapper. |
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192 - Record SignalP version via ``<version_command>``. |
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193 - Internal job splitter will skip starting any pending jobs after a |
31 | 194 child job fails (so the entire task will error out more quickly). |
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195 ======= ====================================================================== |
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196 |
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197 |
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198 Developers |
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199 ========== |
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200 |
25 | 201 This script and other tools were initially developed on the following hg branches: |
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202 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis |
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203 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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204 |
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205 Development has now moved to a dedicated GitHub repository: |
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206 https://github.com/peterjc/pico_galaxy/tree/master/tools |
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207 |
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208 |
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209 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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210 Planemo commands (which requires you have set your Tool Shed access details in |
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211 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
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212 |
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213 $ planemo shed_update -t testtoolshed --check_diff tools/protein_analysis/ |
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214 ... |
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215 |
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216 or:: |
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217 |
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218 $ planemo shed_update -t toolshed --check_diff tools/protein_analysis/ |
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219 ... |
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220 |
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221 To just build and check the tar ball, use:: |
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222 |
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223 $ planemo shed_upload --tar_only tools/protein_analysis/ |
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224 ... |
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225 $ tar -tzf shed_upload.tar.gz |
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226 test-data/Adenovirus.fasta |
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227 test-data/Adenovirus.promoter2.tabular |
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228 test-data/empty.fasta |
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229 test-data/empty_promoter2.tabular |
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230 test-data/empty_psortb_terse.tabular |
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231 test-data/empty_rxlr.Bhattacharjee2006.tabular |
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232 test-data/empty_rxlr.Whisson2007.tabular |
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233 test-data/empty_rxlr.Win2007.tabular |
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234 test-data/empty_signalp3.tabular |
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235 test-data/empty_tmhmm2.tabular |
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236 test-data/empty_wolf_psort.tabular |
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237 test-data/four_human_proteins.fasta |
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238 test-data/four_human_proteins.signalp3.tabular |
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239 test-data/four_human_proteins.tmhmm2.tabular |
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240 test-data/four_human_proteins.wolf_psort.tabular |
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241 test-data/k12_ten_proteins.fasta |
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242 test-data/k12_ten_proteins_psortb_p_terse.tabular |
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243 test-data/rxlr_win_et_al_2007.fasta |
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244 test-data/rxlr_win_et_al_2007.tabular |
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245 test-data/rxlr_win_et_al_2007_sp3.tabular |
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246 tools/protein_analysis/LICENSE.txt |
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247 tools/protein_analysis/README.rst |
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248 tools/protein_analysis/promoter2.py |
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249 tools/protein_analysis/promoter2.xml |
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250 tools/protein_analysis/psortb.py |
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251 tools/protein_analysis/psortb.xml |
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252 tools/protein_analysis/rxlr_motifs.py |
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253 tools/protein_analysis/rxlr_motifs.xml |
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254 tools/protein_analysis/seq_analysis_utils.py |
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255 tools/protein_analysis/signalp3.py |
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256 tools/protein_analysis/signalp3.xml |
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257 tools/protein_analysis/suite_config.xml |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
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258 tools/protein_analysis/tmhmm2.py |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
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259 tools/protein_analysis/tmhmm2.xml |
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260 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm |
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261 tools/protein_analysis/wolf_psort.py |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
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262 tools/protein_analysis/wolf_psort.xml |
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263 |
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264 This simplifies ensuring a consistent set of files is bundled each time, |
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265 including all the relevant test files. |