Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README.rst @ 21:238eae32483c draft

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"Check this is up to date with all 2020 changes (black etc)"
author peterjc
date Thu, 17 Jun 2021 08:21:06 +0000
parents a19b3ded8f33
children e1afa4b0b682
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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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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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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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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 2010-2015 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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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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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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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 https://doi.org/10.7717/peerj.167
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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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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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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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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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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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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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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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75 * ``tmhmm2.xml`` (Galaxy tool definition)
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76 * ``tmhmm2.py`` (Python wrapper script)
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78 * ``signalp3.xml`` (Galaxy tool definition)
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79 * ``signalp3.py`` (Python wrapper script)
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81 * ``promoter2.xml`` (Galaxy tool definition)
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82 * ``promoter2.py`` (Python wrapper script)
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84 * ``psortb.xml`` (Galaxy tool definition)
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85 * ``psortb.py`` (Python wrapper script)
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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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90 * ``rxlr_motifs.xml`` (Galaxy tool definition)
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91 * ``rxlr_motifs.py`` (Python script)
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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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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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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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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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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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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 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).
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180 - Record version of Promoter 2 via ``<version_command>``.
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f3ecd80850e2 v0.2.9 Python style improvements
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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
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194 child job fails (so the entire task will error out more quickly).
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238eae32483c "Check this is up to date with all 2020 changes (black etc)"
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195 v0.2.12 - Fix reporting of HMMER error in RXLR tool.
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196 - Quote command line arguments when RXLR tool calls SignalP.
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197 - Reduce number of temp files if SignalP is run with one thread.
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198 ======= ======================================================================
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199
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200
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201 Developers
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202 ==========
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203
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204 This script and other tools were initially developed on the following hg branches:
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205 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
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206 http://bitbucket.org/peterjc/galaxy-central/src/tools
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207
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208 Development has now moved to a dedicated GitHub repository:
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209 https://github.com/peterjc/pico_galaxy/tree/master/tools
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210
18
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211
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212 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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213 Planemo commands (which requires you have set your Tool Shed access details in
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214 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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215
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216 $ planemo shed_update -t testtoolshed --check_diff tools/protein_analysis/
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217 ...
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218
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219 or::
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220
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221 $ planemo shed_update -t toolshed --check_diff tools/protein_analysis/
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222 ...
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223
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224 To just build and check the tar ball, use::
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225
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226 $ planemo shed_upload --tar_only tools/protein_analysis/
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227 ...
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228 $ tar -tzf shed_upload.tar.gz
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229 test-data/Adenovirus.fasta
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230 test-data/Adenovirus.promoter2.tabular
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231 test-data/empty.fasta
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232 test-data/empty_promoter2.tabular
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233 test-data/empty_psortb_terse.tabular
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234 test-data/empty_rxlr.Bhattacharjee2006.tabular
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235 test-data/empty_rxlr.Whisson2007.tabular
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236 test-data/empty_rxlr.Win2007.tabular
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237 test-data/empty_signalp3.tabular
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238 test-data/empty_tmhmm2.tabular
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239 test-data/empty_wolf_psort.tabular
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240 test-data/four_human_proteins.fasta
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241 test-data/four_human_proteins.signalp3.tabular
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242 test-data/four_human_proteins.tmhmm2.tabular
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243 test-data/four_human_proteins.wolf_psort.tabular
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244 test-data/k12_ten_proteins.fasta
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245 test-data/k12_ten_proteins_psortb_p_terse.tabular
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246 test-data/rxlr_win_et_al_2007.fasta
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247 test-data/rxlr_win_et_al_2007.tabular
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248 test-data/rxlr_win_et_al_2007_sp3.tabular
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249 tools/protein_analysis/LICENSE.txt
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250 tools/protein_analysis/README.rst
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251 tools/protein_analysis/promoter2.py
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252 tools/protein_analysis/promoter2.xml
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253 tools/protein_analysis/psortb.py
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254 tools/protein_analysis/psortb.xml
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255 tools/protein_analysis/rxlr_motifs.py
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256 tools/protein_analysis/rxlr_motifs.xml
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257 tools/protein_analysis/seq_analysis_utils.py
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258 tools/protein_analysis/signalp3.py
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259 tools/protein_analysis/signalp3.xml
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260 tools/protein_analysis/suite_config.xml
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261 tools/protein_analysis/tmhmm2.py
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262 tools/protein_analysis/tmhmm2.xml
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263 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
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264 tools/protein_analysis/wolf_psort.py
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265 tools/protein_analysis/wolf_psort.xml
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266
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267 This simplifies ensuring a consistent set of files is bundled each time,
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268 including all the relevant test files.